Table 4.

Association between each variant and LBD subtype (brainstem, transitional, or diffuse)

						Fraction (%) of patients with diffuse LBD		Association with LBD subtype
Variant	Nearest gene	Chr.	Position	MA	MAF	Minor allele not present	Minor allele present	OR (95% CI)	P-value
rs10788972	TCEANC2	1	54572243	A	47.5%	86/159 (54.1%)	201/387 (51.9%)	0.97 (0.68, 1.38)	0.85
rs35749011	GBA/SYT11	1	155135036	A	2.7%	268/517 (51.8%)	20/30 (66.7%)	1.75 (0.82, 3.75)	0.15
rs114138760	GBA/SYT11	1	154925709	C	1.8%	275/524 (52.5%)	11/20 (55.0%)	1.11 (0.46, 2.65)	0.82
rs823118	RAB7L1/NUCKS1	1	205723572	C	44.8%	88/170 (51.8%)	200/377 (53.1%)	1.09 (0.77, 1.55)	0.62
rs10797576	SIPA1L2	1	232664611	T	13.9%	215/402 (53.5%)	73/145 (50.3%)	0.87 (0.60, 1.25)	0.44
rs6430538	ACMSD/TMEM163	2	135539967	T	43.4%	103/186 (55.4%)	185/361 (51.2%)	0.93 (0.66, 1.31)	0.69
rs1955337	STK39	2	168272635	A	12.5%	216/417 (51.8%)	72/130 (55.4%)	1.14 (0.78, 1.67)	0.50
rs12637471	MCCC1	3	182762437	A	20.3%	187/347 (53.9%)	101/200 (50.5%)	0.93 (0.67, 1.31)	0.68
rs34311866	TMEM175/GAK/DGKQ	4	951947	C	24.4%	168/319 (52.7%)	119/224 (53.1%)	1.07 (0.77, 1.50)	0.67
rs34884217	TMEM175/GAK/DGKQ	4	950422	G	8.4%	238/459 (51.9%)	50/88 (56.8%)	1.17 (0.75, 1.82)	0.50
rs11724635	BST1	4	15737101	C	43.3%	78/165 (47.3%)	196/361 (54.3%)	1.20 (0.84, 1.71)	0.32
rs6812193	FAM47E/SCARB2	4	77198986	T	37.6%	116/214 (54.2%)	172/333 (51.7%)	0.91 (0.65, 1.27)	0.56
rs356182	SNCA	4	90626111	G	35.4%	117/223 (52.5%)	169/321 (52.6%)	0.95 (0.68, 1.33)	0.77
rs3910105	SNCA	4	89761420	C	49.1%	79/138 (57.2%)	205/403 (50.9%)	0.79 (0.54, 1.16)	0.23
rs9275326	HLA-DQB1	6	32666660	T	8.5%	240/456 (52.6%)	47/90 (52.2%)	0.95 (0.61, 1.47)	0.81
rs13201101	HLA-DQB1	6	32375827	T	5.2%	261/496 (52.6%)	26/49 (53.1%)	1.04 (0.59, 1.84)	0.90
rs199347	GPNMB	7	23293746	C	38.5%	113/206 (54.9%)	174/339 (51.3%)	0.92 (0.66, 1.29)	0.63
rs591323	FGF20	8	16697091	T	25.6%	162/309 (52.4%)	125/237 (52.7%)	1.04 (0.75, 1.44)	0.81
rs117896735	INPP5F	10	119776815	A	1.2%	268/508 (52.8%)	5/12 (41.7%)	0.61 (0.21, 1.79)	0.37
rs329648	MIR4697	11	133765367	T	35.5%	109/226 (48.2%)	179/321 (55.8%)	1.41 (1.01, 1.96)	0.041
rs76904798	LRRK2	12	40614434	T	13.5%	224/407 (55.0%)	63/139 (45.3%)	0.67 (0.46, 0.97)	0.034
rs11060180	CCDC62	12	123303586	G	48.0%	80/149 (53.7%)	208/398 (52.3%)	0.97 (0.67, 1.40)	0.86
rs11158026	GCH1	14	55348869	T	32.7%	124/241 (51.5%)	164/306 (53.6%)	1.09 (0.79, 1.51)	0.61
rs2414739	VPS13C	15	61994134	G	28.3%	141/270 (52.2%)	147/277 (53.1%)	0.94 (0.68, 1.30)	0.69
rs14235	BCKDK/STX1B	16	31121793	A	41.5%	90/191 (47.1%)	198/356 (55.6%)	1.45 (1.03, 2.03)	0.032
rs11868035	SREBF/RAI1	17	17715101	A	31.6%	136/258 (52.7%)	152/289 (52.6%)	1.00 (0.72, 1.38)	0.98
rs17649553	MAPT	17	43994648	A	22.8%	164/331 (49.5%)	123/214 (57.5%)	1.39 (0.99, 1.95)	0.054
rs12456492	RIT2	18	40673380	G	30.9%	131/257 (51.0%)	156/289 (54.0%)	1.14 (0.83, 1.59)	0.42
rs55785911	DDRGK1	20	3168166	A	37.2%	116/215 (54.0%)	169/328 (51.5%)	0.87 (0.62, 1.22)	0.42

Chr=chromosome; MA=minor allele; MAF=minor allele frequency; OR: odds ratio; CI=confidence interval. LB=Lewy body. ORs, 95% CIs, and p-values result from proportional odds logistic models adjusted for age at death and sex. ORs are interpreted as the multiplicative increase in the odds of a more widespread distribution of LB pathology (i.e. diffuse more than transitional more than brainstem) corresponding to presence of the minor allele. The proportion of patients with diffuse LBD is given for illustrative purposes, however LBD subtype (brainstem, transitional, diffuse) was analyzed as an ordered categorical variable in proportional odds logistic regression analysis. After applying a Bonferroni correction for multiple testing, p-values of 0.0017 or lower are considered as statistically significant. Variants shown in bold are those with a nominally significant (P≤0.05) association.