Extended Data Table 3. Genome-wide significant (P<5x10^-8) and suggestive (P<1x10^-5) signals in our AD-PID and Li et al. (Nat Comm, 2015) CVID GWAS meta-analysis.

The AD-PID WGS cohort included 733 cases and 9225 controls, whereas the CVID Immunochip cohort included 778 cases and 10999 controls. The total number of shared meta-analysed variants was 95417. P-values are adjusted for individual study genomic inflation factor lambda. The selection of genes from each locus used in COGS analysis is described in Methods and Supplementary Note 3.

Locus	Lead SNP	Chr	Position (GRCh37)	Effect allele	OR AD-PID	P AD-PID	OR Li et al.	P Li et al.	OR Meta	P Meta	Genes in COGS analysis	Nearest Gene (dist. to lead SNP, bp)
Genome-wide significant signals in MAF>5% meta-analysis
6p21.33	rs2517529	6	31076978	G	1.39	1.30x10-09	1.41	1.96x10-10	1.40	1.5x10-18	-	C6orf15 (2021)
16p13.13	rs2286974	16	11114512	G	0.77	6.23x10-06	0.73	6.18x10-08	0.75	2.2x10-12	PRM2, RMI2, PRM3, TNP2, SOCS1	CLEC16A (0)
Additional suggestive signals in MAF>5% meta-analysis
3p24.1	rs3806624	3	27764623	A	1.19	2.43x10-03	1.29	3.41x10-06	1.20	5.3x10-08	SLC4A7, TOP2B, SGOL1, NGLY1, OXSM, NEK10, EOMES, AZI2, CMC1, ZCWPW2	EOMES (416)
18p11.21	rs80191532	18	12752868	T	1.47	9.14x10-07	1.18	5.06x10-02	1.30	9.3x10-07	SEH1L, RNMT, LDLRAD4, PTPN2, FAM210A	PSMG2 (27128)
1q31.3	rs12563449	1	198427282	T	0.87	7.66x10-02	0.56	2.13x10-08	0.74	1.3x10-07	LHX9, NEK7, C1orf53	ATP6V1G3 (65069)
11q24.3	rs10750403	11	128477472	C	1.17	4.07x10-03	1.21	5.13x10-04	1.20	7.0x10-06	ETS1	ETS1 (20018)
14q13.2	rs11851820	14	35803517	T	0.69	1.29x10-02	0.15	2.47x10-08	0.54	7.1x10-06	NFKBIA	PSMA6 (16817)
Additional AD-PID genome-wide significant signal in MAF>0.5% GWAS
17p11.2	rs34557412	17	16852187	G	4.04	1.37x10-12	-	-	-	-	-	TNFRSF13B (0)