Table 2.

Significant variants reported by Ref.⁷.

Locus						Base GWAS7		UKBB GWAS of AD PRS extremes			Stage 18
CHR	Position	A2	A1	Nearest gene	SNP	OR	p value	OR	p value	Lowest p value variant at locus	Lowest p value variant at locus
1	161155392	G	A	ADAMTS4	rs4575098	1.02	2.05E−10	1.16	6.90E−18	rs4575098 (6.90E−18)	rs72702127 (3.03E−4)
1	207786828	G	A	CR1	rs2093760	1.02	1.10E−18	1.21	1.64E−23	rs4844610 (4.87E−25)	rs679515 (1.56E−16)
2	127891427	A	C	BIN1	rs4663105	1.03	3.38E−44	1.17	1.57E−24	rs4663105 (1.57E−24)	rs6733839 (4.02E−28)
2	233981912	C	G	INPP5D	rs10933431	0.98	8.92E−10	0.90	8.91E−10	rs36133610 (4.78E−14)	rs10933431 (2.55E−7)
3	57226150	C	T	HESX1	rs184384746	1.22	1.24E−08	–	–	rs79762933 (1.08E−9)	rs1565377 (4.67E−4)
4	11026028	G	A	CLNK	rs6448453	1.01	1.93E−09	1.09	4.75E−07	rs55706526 (3.87E−7)	rs4351014 (1.96E−5)
4	11723235	G	A	HS3ST1	rs7657553	1.01	0.051	1.02	0.19	rs55706526 (3.87E−7)	rs4351014 (1.96E−5)
6	32583357	A	T	HLA-DRB1	rs6931277	1.00	8.41E−11	0.82	3.73E−25	rs9274812 (1.87E−33)	rs201239900 (2.24E−9)
6	40942196	G	A	TREM2	rs187370608	1.26	1.45E−16	–	–	rs9394764 (1.01E−9)	rs75932628 (2.95E−12)
6	47432637	T	C	CD2AP	rs9381563	1.01	2.52E−10	1.11	6.13E−12	rs1385742 (7.24E−13)	rs1385742 (2.23E−8)
7	99971834	G	A	ZCWPW1/PILRA	rs1859788	0.98	2.22E−15	0.82	1.72E−35	rs2906657 (2.08E−36)	rs60738304 (1.15E−5)
7	143108158	C	T	EPHA1	rs7810606	0.99	3.59E−11	0.90	3.72E−13	rs7810606 (3.72E−13)	rs11767557 (1.56E−8)
7	145950029	C	T	CNTNAP2	rs114360492	1.20	2.10E−09	–	–	rs73742508 (4.24E−4)	rs62483962 (1.83E−4)
8	27464929	G	A	CLU/PTK2B	rs4236673	0.98	2.61E−19	0.93	8.46E−07	rs57735330 (6.52E−19)	rs867230 (3.49E−17)
10	11717397	T	C	ECHDC3	rs11257238	1.01	1.26E−08	1.08	2.14E−07	rs7912495 (9.20E−9)	rs12416487 (3.42E−8)
11	59958380	C	A	MS4A6A	rs2081545	0.98	1.55E−15	0.87	6.65E−21	rs367670643 (2.36E−21)	rs1582763 (1.19E−16)
11	85776544	A	G	PICALM	rs867611	0.98	2.19E−18	0.84	7.21E−29	rs10792832 (6.03E−31)	rs3851179 (5.81E−16)
11	121435587	T	C	SORL1	rs11218343	0.96	1.09E−11	–	–	rs1133174 (1.21E−5)	rs11218343 (2.63E−8)
14	92938855	G	A	SLC24A4	rs12590654	0.99	1.65E−10	0.91	1.29E−08	rs35627364 (1.59E−10)	rs12590654 (8.73E−9)
15	59022615	T	C	ADAM10	rs442495	0.99	1.31E−09	0.91	8.52E−10	rs602602 (1.04E−13)	rs383902 (3.81E−6)
15	63569902	C	T	APH1B	rs117618017	1.01	3.35E−08	1.10	4.60E−06	rs4984289 (1.79E−16)	rs12913805 (1.59E−5)
16	31133100	G	A	KAT8	rs59735493	0.99	3.98E−08	0.91	4.90E−09	rs7499339 (5.76E−14)	rs201827363 (2.06E−3)
17	5138980	G	A	SCIMP	rs113260531	1.02	9.16E−10	1.15	8.13E−10	rs78538460 (2.48E−12)	rs61182333 (2.18E−5)
17	47450775	G	A	ABI3	rs28394864	1.01	1.87E−08	1.07	1.40E−05	rs850522 (6.57E−10)	rs2960170 (1.52E−3)
17	56409089	G	C	BZRAP1-AS1	rs2632516	0.99	9.66E−07	0.93	3.68E−06	rs1985749 (1.15E−7)	rs2632516 (3.67E−7)
18	29088958	C	T	SUZ12P1	rs8093731	0.98	0.03	–	–	rs7240561 (9.92E−5)	rs189640326 (3.18E−4)
18	56189459	T	C	ALPK2	rs76726049	1.06	3.30E−08	–	–	rs35597325 (5.59E−5)	rs187113635 (1.08E−4)
19	1039323	C	G	ABCA7	rs111278892	1.02	7.93E−11	1.15	1.18E−11	rs3752231 (1.84E−12)	rs12151021 (2.56E−10)
19	45351516	C	G	APOE	rs41289512	1.23	5.79E−276	3.44	5.64E−212	rs814573 (1.62E−673)	rs429358 (1.17E−881)
19	46241841	C	T	AC074212.3	rs76320948	1.04	4.64E−08	–	–	rs123187 (8.72E−27)	rs181476525 (8.29E−13)
19	51727962	C	A	CD33	rs3865444	0.99	6.34E−09	0.94	4.74E−05	rs1354106 (1.13E−5)	rs3865444 (3.93E−7)
20	54998544	A	G	CASS4	rs6014724	0.98	6.56E−10	0.92	1.88E−03	rs1059768 (2.56E−7)	rs6014724 (3.65E−7)

Lowest p value columns are defined as 500 kb flanking the original reported variant. SNP positions are in GRCh37/hg19.