Table 2.

Novel shared SNP’s between ASD and INT, and ASD and EDU found through cond/conjFDR.

Chr	Min-max BPs	Lead SNPs	conjFDR	ASD		Trait (INT/EDU)
				Z-score	p-value	Z-score	p-value	Concordant	Overlapping
ASD and INT
3	16843737-16879208	rs7625233	0.042	3.9	1.14E−04	−4.88	1.07E−06	No	Yes
3	48564209-50239012	rs73073015	0.020	4.1	3.51E−05	6.28	3.43E−10	Yes	Yes
5	81261923-81679914	rs73134709	0.041	−3.9	9.58E−05	−3.86	1.16E−04	Yes	No
5	92488009-92574385	rs4242244	0.036	−3.9	8.64E−05	−5.48	4.16E−08	Yes	Yes
5*	113837198-113995764	rs414517	0.016	−4.23	2.30E−05	−4.25	2.18E−05	Yes	No
8	87754626-87783335	rs1982564	0.038	3.90	9.62E−05	−4.01	6.14E−05	No	Yes
10	106563924-106830537	rs6584649	0.046	−3.82	1.33E−04	3.88	1.05E−04	No	No
10	133729181-133815530	rs34473884	0.018	4.17	3.03E−05	5.26	1.48E−07	Yes	Yes
14	29396922-29677464	rs140802584	0.034	4.02	5.87E−05	−3.93	8.42E−05	No	No
17	43463493-44865603	rs7207582	0.002	4.71	2.44E−06	−4.91	9.22E−07	No	No
21	40553845-40741068	rs2249666	0.039	3.89	9.89E−05	4.06	4.99E−05	Yes	No
ASD and EDU
1	45797505-46021556	rs12049503	0.050	3.77	1.63E−04	4.10	4.12E−05	Yes	No
2*	104056454-104387855	rs6543224	0.015	4.26	2.05E−05	5.01	5.32E−07	Yes	No
2	159340038-159553686	rs3771643	0.049	3.80	1.46E−04	3.97	7.29E−05	Yes	No
2	215361613-215406125	rs12467438	0.044	−3.84	1.25E−04	4.28	1.85E−05	NO	No
3	16843737-16879208	rs7625233	0.042	3.86	1.14E−04	−6.37	1.83E−10	No	Yes
3	48564209-50239012	rs73073015	0.021	4.14	3.51E−05	7.25	4.14E−13	Yes	Yes
3	70252572-70291268	rs73116288	0.019	4.18	2.93E−05	4.53	5.89E−06	Yes	No
3	157829953-158284861	rs7630176	0.050	−3.77	1.63E−04	4.13	3.58E−05	No	No
4	105319081-105414222	rs7665487	0.037	3.91	9.27E−05	−4.28	1.84E−05	No	No
5	87792844-87932809	rs4916723	0.002	4.76	1.92E−06	−7.09	1.32E−12	No	No
5	92488009-92574385	rs4242244	0.036	−3.93	8.64E−05	−5.04	4.75E−07	Yes	Yes
5	113788755-113995764	rs13188074	0.004	4.67	3.04E−06	5.30	1.18E−07	Yes	No
6	19211776-19358341	rs7762189	0.048	3.79	1.51E−04	−4.60	4.25E−06	No	No
6	26341301-26341301	rs9467715	0.049	−3.78	1.60E−04	−5.42	5.98E−08	Yes	No
7*	24526039-24536700	rs6461809	0.012	4.33	1.48E−05	6.04	1.55E−09	Yes	No
8	87754626-87783335	rs1982564	0.038	3.90	9.62E−05	−5.46	4.75E−08	No	Yes
10	133729181-133815530	rs34473884	0.020	4.17	3.03E−05	7.40	1.32E−13	Yes	Yes
11	17804998-17852452	rs2237944	0.042	3.85	1.18E−04	4.69	2.69E−06	Yes	No
13	58746132-59167198	rs77146055	0.044	3.83	1.26E−04	−4.02	5.90E−05	No	No
17	2295405-2296014	rs2447091	0.041	3.87	1.09E−04	−4.68	2.89E−06	No	No
17*	43463493-44865603	rs55915917	0.004	4.64	3.55E−06	−8.39	4.93E−17	No	No

Chr Chromosome, Min-max BPs Minimum-Maximum Base Pairs, Lead SNP Single Nucleotide Polymorphism within a locus having the lowest P-value, conjFDR Conjunctional False Discovery Rate, ASD Autism Spectrum Disorder, INT Intelligence, EDU Educational attainment, Overlapping overlapping SNP’s between INT and EDU.

*Loci with significant local genetic correlation.