. Author manuscript; available in PMC: 2021 Mar 25.

Published in final edited form as: Nat Genet. 2020 Nov 23;52(12):1314–1332. doi: 10.1038/s41588-020-00713-x

Table 3. Newly identified independent BP-associated rare SNVs (MAF ≤ 0.01) at known loci in UK Biobank only.

Locus ID	rsID	Chr:Position	Gene	Info	EA/OA	Consequence	Trait	Unconditional SNV analysis			FINEMAP output			Ref
Locus ID	rsID	Chr:Position	Gene	Info	EA/OA	Consequence	Trait	EAF	β	P-value	Common SNVs in top configuration	PP of n SNVs	log₁₀BF	Ref
5	rs41300100	1:11908146	NPPA	0.82	G/C	5’ UTR	SBP	0.010	-0.10	4.70x10^-21	rs2982373, rs5066, rs55892892	0.55	122.50	^9,2,79
18	rs756799918	1:153464738	RN7SL44P	0.89	T/C	intergenic	SBP	0.0004	0.26	4.30x10^-7	rs12030242	0.36	27.49	¹⁴
28	rs1805090	1:230840034	AGT	NA	T/G	missense	SBP	0.0025	0.11	6.80x10^-8	rs3889728, rs2493135	0.79	26.23	⁸
28	rs539645495	1:230860071	RP11-99J16__A.2	0.97	G/A	intron, non-coding transcript	DBP	0.0024	0.13	3.20x10^-9	rs2493135, rs3889728	0.83	30.97	⁸
33	rs56152193	2:20925891	LDAH	0.76	C/G	intron	PP	0.0006	-0.23	8.10x10^-7	rs7255	0.36	17.95	^{17, 16}
55	rs759606582	2:178325956	AGPS	0.96	G/A	intron	PP	0.0003	0.29	1.90x10^-7	rs56726187	0.57	7.48	¹⁶
72	rs555934473	3:48899332	SLC25A20	0.74	T/G	intron	DBP	0.0012	-0.17	2.50x10^-6	rs36022378, rs6442105, rs6787229	0.25	35.71	^{17, 16, 6, 11}
73	rs76920163	3:53857055	CHDH	0.96	G/T	intron	SBP	0.0059	0.10	3.80x10^-13	rs3821843, rs7340705, rs11707607	0.58	29.45	^{18, 16}
	rs144980716	3:53776904	CACNA1D	0.91	A/G	intron	PP	0.0065	0.07	2.60x10^-8	rs36031811, rs77347777	0.57	18.42
85	rs547947160	3:141607335	ATP1B3	0.75	G/A	intron	PP	0.0008	0.20	6.00x10^-6	rs6773662	0.54	7.040	¹³
86	rs545513277	3:143113550	SLC9A9	0.70	A/G	intron	PP	0.0006	-0.24	6.90x10^-6	rs1470121	0.56	11.97	¹⁶
92	rs186525102	3:185539249	IGF2BP2	0.85	A/G	intron	SBP	0.0086	-0.06	6.70x10^-7	rs4687477	0.56	8.08	¹⁷
94	rs111620813	4:8293193	HTRA3	NA	A/G	missense	PP	0.0100	-0.05	2.00x10^-6	rs28734123	0.53	12.54	¹⁸
132	rs181585444	5:129963509	AC005741.2	0.83	C/T	intergenic	DBP	0.0003	-0.30	3.80x10^-6	rs274555	0.55	10.70	^{14, 13}
137	rs546907130	6:8156072	EEF1E1	0.90	T/C	intergenic	SBP	0.0017	-0.14	1.90x10^-7	rs3812163	0.70	8.57	¹⁶
141	rs72854120	6:39248533	KCNK17	0.91	C/T	intergenic	SBP	0.0073	-0.08	3.10x10^-9	rs2561396	0.76	10.49	¹⁶
141	rs72854118	6:39248092	KCNK17	0.91	G/A	intergenic	DBP	0.0072	-0.07	2.70x10^-7	rs1155349	0.85	11.12	¹⁶
164	rs138890991	7:40804309	SUGCT	0.94	C/T	intron	PP	0.0100	0.06	1.60x10^-7	rs17171703	0.77	19.08	¹⁷
179	rs561912039	7:150682950	NOS3	0.74	T/C	intergenic	DBP	0.0017	-0.13	6.40x10^-6	rs3793341, rs3918226, rs6464165, rs7788497, rs891511	0.34	81.75	^9,14,10
183	rs570342886	8:23380012	SLC25A37	0.85	C/G	intergenic	DBP	0.0001	-0.48	9.80x10^-7	rs7842120	0.58	15.74	¹⁶
190	rs201196388	8:95265263	GEM	NA	T/C	splice donor	PP	0.0005	0.26	2.40x10^-9	rs2170363	0.34	31.80	^{16, 78}
193	rs532252660	8:120587297	ENPP2	0.79	T/C	intron	DBP	0.0025	-0.11	4.10x10^-7	rs7017173	0.81	26.53	⁶
193	rs181416549	8:120678125	ENPP2	0.84	A/G	intron	PP	0.0026	0.20	5.10x10^-21	rs35362581, rs80309268	0.95	113.21	⁶
212	rs138765972	10:20554597	PLXDC2	0.94	C/T	intron	DBP	0.0075	-0.07	4.40x10^-8	rs61841505	0.49	9.06	¹⁶
219	rs192036851	10:64085523	RP11-120C12.3	0.92	C/T	intergenic	SBP	0.0062	0.06	6.40x10^-6	rs10995311	0.28	19.55	^{16, 13}
234	rs150090666	11:14865399	PDE3B	NA	T/C	stop gained	DBP	0.0010	-0.16	5.20x10^-7	rs11023147, rs2597194	0.55	12.93	¹⁶
242	rs139620213	11:61444612	DAGLA	0.89	T/C	upstream gene	PP	0.0019	0.11	5.90x10^-6	rs2524299	0.48	6.64	¹⁵
246	rs540659338	11:89183302	NOX4	0.85	C/T	intron	PP	0.0027	-0.14	2.60x10^-10	rs2289125, rs494144	0.62	58.09	^{17, 16}
260	rs186600986	12:53769106	SP1	0.91	A/G	upstream gene	PP	0.0030	-0.09	1.10x10^-6	rs73099903	0.48	12.91	¹⁹
266	rs137937061	12:111001886	PPTC7	0.74	A/G	intron	SBP	0.0048	-0.09	1.30x10^-6	rs9739637, rs35160901, rs10849937, rs3184504	0.34	55.74	^{16, 4, 5}
268	rs190870203	12:123997554	RILPL1	0.85	T/G	intron	PP	0.0020	0.12	1.70x10^-7	rs4759375	0.72	9.50	¹³
270	rs541261920	13:30571753	RP11-629E24.2	0.79	G/C	intergenic	SBP	0.0005	0.24	9.20x10^-6	rs7338758	0.54	10.09	¹⁶
281	rs149250178	14:100143685	HHIPL1	0.75	A/G	3’ UTR	DBP	0.0004	-0.29	2.30x10^-6	rs7151887	0.51	7.93	¹⁶
299	rs139491786	16:2086421	SLC9A3r2	NA	T/C	missense	DBP	0.0068	-0.12	1.60x10^-20	rs28590346, rs34165865, rs62036942, rs8061324	0.57	50.80	¹⁶
304	rs2234710	16:30907835	BCL7C	0.79	T/G	upstream gene	SBP	0.0075	-0.08	2.30x10^-9	-	0.52	6.29	^{17, 16}
304^*	rs148753960	16:31047822	STX4	0.89	T/C	intron	PP	0.0099	-0.07	1.80x10^-9	rs7500719	0.42	12.21	^{17, 16}
317	rs756906294	17:42323081	SLC4A1	0.73	T/C	downstream gene	PP	0.0030	0.01	8.30x10^-6	rs66838809	0.27	18.94	¹⁷
322	rs16946721	17:61106371	TANC2	0.91	G/A	intron	DBP	0.0100	-0.07	1.40x10^-11	rs1867624, rs4291	0.51	20.91	^{17, 16}
333	rs55670943	19:11441374	RAB3D	0.87	C/T	intron	SBP	0.0085	-0.10	2.10x10^-17	rs12976810, rs4804157, rs160838, rs167479	0.78	85.45	^13–15
346^*	rs149972827	20:30413439	MYLK2	0.98	A/G	intron	SBP	0.0036	-0.10	6.20x10^-9	-	0.85	9.86	¹⁶
362	rs115089782	22:42329632	CENPM	0.93	T/C	intergenic	SBP	0.0001	0.53	4.20x10^-6	rs139919	0.44	14.12	^{17, 13}

FINEMAP²⁵ was used to identify the most likely causal variants within the known loci (defined in Supplementary Table 1) using the BOLT-LMM results in UKBB, the full detailed listing of results is provided in Supplementary Table 8. Locus ID, the known locus identifier provided in Supplementary Table 1; Chr:Position, chromosome and physical position in Build 37; Info, imputation information score, NA indicates that the SNV was genotyped and not imputed; EA/OA, Effect allele and other allele, respectively; AA, amino acid change; Effect, predicted effect of the listed SNV; EAF, effect allele frequency; β, single variant effect estimate for the rare variant in the BOLT-LMM analysis; P-value, the single variant P-value from the mixed model in the BOLT-LMM analysis; PP of n SNVs, the posterior probability of the number of causal variants; Log₁₀BF, log₁₀ Bayes factor for the top configuration; Gene, nearest gene; Trait, blood pressure trait analyzed; Ref, reference of the first reports of association in the listed region.

rs540659338 identified in UK Biobank in NOX4 has r ² = 1 in 1000G EUR with rs56061986 identified in the GCTA analysis in Table 4.

Variants at these loci are in LD with GCTA variants (Table 2): at locus 304, r ² = 0.876 between rs148753960 and rs61738491; at locus 346, r ² = 0.952 between rs149972827 and rs45499294.