Table 3.

Set-based association for 23 IGAP loci and the FA feature using all the common variants (MAF ≥ 0.05) in the neighborhood of the identified risk gene corresponding to each AD risk locus. Empirical p-values were calculated using 20,000 permutations in PLINK.

Gene	Number of SNPs in gene	Number of significant SNPs (p < 0.05, r2 < 0.5)	Empirical gene-based p-value	List of significant SNP
CELF1	346	4	8 × 10−4	rs7118178|rs7925299| rs2203712|rs71475924
CLU	539	3	0.0117	rs11135998|rs59953408| rs532754
SORL1	540	5	0.01405	rs664424|rs11600686| rs4372460|rs12276905| rs10790451
PICALM	687	13	0.1529	rs471470|rs67598967| rs6592271|rs11234568| rs598561|rs11607590| rs56302636|rs11234555| rs3862786|rs10792829| rs11234549|rs12277986| rs11825598
FERMT2	486	1	0.2276	rs62003479
HLA-DRB5	373	2	0.2783	rs9271176|rs680151
SLC24A4	1134	10	0.2957	rs79544202|rs12434183| rs9972287|rs34723497| rs1108161|rs55840245| rs4904955|rs12436499| rs66753927|rs55866218
HLA-DRB1	399	2	0.3195	rs9271176|rs680151
EPHA1	450	3	0.3443	rs73154208|rs55893042| rs7810606
CASS4	494	3	0.3445	rs6024817|rs6024937| rs11906849
RIN3	1093	5	0.3584	rs12434183|rs55977629|rs55840245|rs4904955| rs1242105
CD33	320	13	0.3916	rs10425414|rs273692| rs2134068|rs7253654| rs34564964|rs2411329| rs3887787|rs35982135| rs79254320|rs1710353| rs10409348|rs73055137| rs4802772
INPP5D	577	6	0.4419	rs72984219|rs7581670| rs3792106|rs59199559| rs62192899|rs62192926
BIN1	908	3	0.4477	rs6716819|rs6431230| rs13031473
PTK2B	779	13	0.4514	rs17375582|rs2565045| rs2322607|rs11780471| rs11994882|rs2565048| rs2241657|rs7000615| rs1367088|rs187228254| rs7013346|rs2271920| rs2741341
ZCWPW1	234	1	0.5396	rs118119933
CR1	617	3	0.6456	rs61821132|rs1570564| rs71515116
NME8	750	3	0.6471	rs1668347|rs2198050| rs1668357
ABCA7	672	7	0.7435	rs2240615|rs35500465| rs4147940|rs349310| rs8106918|rs4147912| rs7260506
MEF2C	373	3	0.7944	rs7728694|rs214134| rs75034114
CD2AP	884	1	0.8546	rs16876369
DSG2	491	1	0.8602	rs36032521
MS4A6A	403	0	1	NA