Convergent lines of evidence support BIN1 as a risk gene of Alzheimer’s disease

Zhu, Jin; Liu, Xia; Yin, Hongtao; Gao, Yan; Yu, Hao

doi:10.1186/s40246-021-00307-6

Human Genomics

Table 1 Integrative analysis of GWAS and eQTL identified risk genes of AD

From: Convergent lines of evidence support BIN1 as a risk gene of Alzheimer’s disease

Chr	BP	SNP	A1	A2	Gene	b_GWAS	se_GWAS	p_GWAS	b_eQTL	se_eQTL	p_eQTL	b_SMR	se_SMR	p_SMR	p_HEIDI
Integrative analysis of AD GWAS and blood eQTL
1	161156033	rs11585858	A	C	B4GALT3	0.016	0.003	5.58E− 10	− 0.168	0.011	1.07E− 57	− 0.093	0.016	7.33E− 09	3.33E− 03
1	161186313	rs4379692	T	C	NDUFS2	0.012	0.002	8.25E− 08	− 0.231	0.009	4.34E− 132	− 0.053	0.010	1.63E− 07	1.22E− 01
2	127839474	rs11682128	A	G	BIN1	0.031	0.006	2.21E− 08	0.742	0.009	0.00E+ 00	0.042	0.008	2.36E− 08	2.12E− 03
6	32573415	rs601945	G	A	HLA-DRA	− 0.019	0.003	1.38E− 10	− 0.117	0.014	1.39E− 16	0.160	0.032	3.99E− 07	4.25E− 03
7	99803412	rs2950517	G	C	CASTOR3	− 0.014	0.002	2.15E− 09	0.124	0.009	3.30E− 42	− 0.114	0.021	4.26E− 08	8.74E− 03
7	143104331	rs3935067	C	G	EPHA1-AS1	0.015	0.002	6.52E− 11	− 0.466	0.011	0.00E+ 00	− 0.031	0.005	1.11E− 10	6.94E− 03
14	92955385	rs17783630	C	A	SLC24A4	0.011	0.002	6.71E− 07	− 0.503	0.008	0.00E+ 00	− 0.021	0.004	7.31E− 07	3.28E− 02
14	92955385	rs17783630	C	A	RIN3	0.011	0.002	6.71E− 07	− 0.165	0.009	9.12E− 77	− 0.064	0.013	1.58E− 06	6.15E− 02
15	63571820	rs75763893	T	C	APH1B	0.017	0.003	9.15E− 08	0.681	0.018	0.00E+ 00	0.025	0.005	1.22E− 07	5.00E− 02
17	5014212	rs73976310	A	G	AC012146.7	0.018	0.003	7.04E− 08	− 0.743	0.013	0.00E+ 00	− 0.024	0.004	8.00E− 08	1.55E− 02
17	5014212	rs73976310	A	G	ZNF232	0.018	0.003	7.04E− 08	− 0.305	0.013	8.16E− 114	− 0.058	0.011	1.57E− 07	7.88E− 02
19	51731176	rs7245846	A	G	SIGLEC22P	− 0.012	0.002	1.19E− 07	0.166	0.009	2.38E− 70	− 0.072	0.014	3.91E− 07	1.05E− 01
19	51726911	rs1710398	C	A	CD33	0.011	0.002	4.46E− 07	0.290	0.009	3.60E− 221	0.037	0.007	6.18E− 07	4.27E− 03
20	54989833	rs6014722	A	T	CASS4	− 0.022	0.004	2.62E− 09	− 0.141	0.016	3.81E− 19	0.159	0.032	7.20E− 07	4.18E− 03
20	54987216	rs17462136	C	G	RPL39P	− 0.022	0.004	6.43E− 09	− 0.208	0.017	5.07E− 33	0.106	0.020	1.76E− 07	2.50E− 03
Integrative analysis of AD GWAS and brain eQTL
1	207750568	rs679515	C	T	CR1	− 0.025	0.003	1.10E− 18	− 0.587	0.067	2.10E− 18	0.042	0.007	5.17E− 10	4.67E− 02
17	5014212	rs73976310	G	A	AC012146.7	− 0.018	0.003	7.04E− 08	0.721	0.062	6.19E− 31	− 0.025	0.005	1.03E− 06	2.73E− 01

We used the blood eQTL results of eQTLGen consortium [18], and the brain eQTL data from the study by Qi et al. [19]. Chr chromosome, BP base position, Gene gene symbol, A1 reference allele, A2 alternative allele, b_GWAS regression coefficient for AD (positive value indicates increased risk for AD in carriers of the alternative allele and negative value represents decreased risk for AD), se_GWAS standard error in GWAS, p_GWAS p value of GWAS, b_eQTL beta value of eQTL (positive values indicate increased expression with alternative allele and negative value represents decreased expression level), se_eQTL standard error of eQTL, p_eQTL p value of eQTL, b_SMR beta value of SMR test (positive values indicate increased expression level of target gene contributed to the risk of AD and negative values represent the opposite results), se_SMR standard error of SMR test, p_SMR p value of SMR test

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ISSN: 1479-7364

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