Table 2. Number of gene expression-by-SNP associations at various levels of significance.

Significance level	Minimum R2 $	Total number of associations	cis/trans ratio for associations	Total number of associated expressions (eQTLs)	cis/trans ratio for eQTLs	Total number of associated SNPs (eSNPs)	cis/trans ratio for eSNPs
<10−6	0.016	93491	2.1	8575	0.5	67190	2.4
<10−8	0.022	54749	7.3	3857	3.0	41425	11.2
<10−10	0.028	42421	9.8	2998	6.0	33339	16.3
<5.78×10−12	0.031	37403	10.7	2745	7.1	29912	17.1
<10−15	0.042	27330	12.7	2180	9.5	22591	17.8
<10−20	0.057	19655	14.7	1725	12.8	16883	19.2
<10−25	0.071	15015	16.4	1429	16.2	13045	21.5
<10−35	0.099	9673	17.1	1031	21.6	8516	22.9
<10−50	0.140	5873	14.0	712	28.8	5224	21.7
<10−100	0.263	1790	10.5	290	28.1	1598	11.1
<10−150	0.371	922	5.5	156	21.4	772	5.9
<10−200	0.463	635	3.7	97	15.3	504	3.9
<10−300	0.606	321	1.7	38	11.7	213	1.7

^$ Minimum R² (proportion of gene expression variability explained by a SNP) observed for a given significance level. Numbers corresponding to study-wise significance are shown in bold. For investigating cis associations or performing any other hypothesis-based test, lower levels of significance may be considered.