Table 1 Distribution of SNPs, genes and eQTL across chromosomes

CHR	Genotyped SNPs	1000G Imputed SNPs	SNPs MAF > 0.05	Genes	cis-eQTL SNPs^a	eGenes^b	cis-eQTL / gene	trans-eQTL SNPs^c
1	63,788	2,355,554	500,136	1548	2226	34	65.5
2	66,223	2,583,715	541,685	1019	2110	30	70.3	71
3	54,141	2,168,103	466,623	850	529	16	33.1
4	49,864	2,168,950	483,706	606	573	14	40.9	57
5	50,522	1,990,693	420,406	683	1244	16	77.8
6	50,532	1,926,303	450,052	814	3344	26	128.6	2791
7	42,042	1,753,429	387,420	737	3025	26	116.3	1
8	43,775	1,715,508	358,977	532	1270	12	105.8
9	36,939	1,298,383	281,170	603	610	14	43.6
10	43,414	1,486,816	335,916	582	763	18	42.4
11	39,718	1,485,686	325,463	899	1085	19	57.1
12	38,043	1,440,247	316,735	781	1414	18	78.6	66
13	30,842	1,086,129	244,462	268	460	8	57.5
14	25,227	989,387	216,774	501	890	11	80.9
15	23,462	883,939	187,482	489	576	5	115.2
16	24,942	942,939	198,649	684	347	12	28.9
17	18,379	818,215	177,606	924	2957	22	134.4	7474
18	23,775	855,576	187,532	211	296	4	74.0
19	10,429	652,249	155,600	1034	1418	22	64.5
20	20,617	668,157	145,784	417	923	7	131.9
21	11,323	409,662	95,007	157	317	4	79.3
22	10,169	394,297	91,478	379	1454	15	96.9	204
X	32,089	958,335	194,730	580	1236	10	123.6
All	810,255	31,032,272	6,763,393	15,298	29,067	363	80.1	10,664

MAF minor allele frequency, SNPs single nucleotide polymorphisms, TSS transcription start site
^acis-eQTL within 1 Mb of the TSS with nominal p < 2e-10 (adjusted p < 0.01)
^b eGenes: unique genes with significant eQTL
^ctrans-eQTL with nominal p < 4e-13 (adjusted p < 0.01)

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