Table 1 Comparison of cis-eQTL summary statistics using mm9 vs mm10.

Assembly	Liver NSD		Liver SD		Cortex NSD		Cortex SD
Assembly	mm9	mm10	mm9	mm10	mm9	mm10	mm9	mm10
Total genes	14103	12647	14103	12647	14889	15734	14889	15734
Unique genes	2405	949	2405	949	1043	1888	1043	1888
Genes with significant cis-eQTL	3155	3092	2654	2695	4522	4192	4732	4542
Proportion of genes with significant cis-eQTL	0.22	0.24	0.19	0.21	0.30	0.27	0.32	0.29
Genes with significant cis-eQTL overlapping	2255		1911		3204		3483
Genes with not significant cis-eQTL overlapping	8375		8857		9062		8801
Genes with significant cis-eQTL not overlapping	900	837	743	784	1318	988	1249	1059
Genes with significant cis-eQTL almost overlapping	2995	2898	2535	2505	4201	4019	4441	4350

‘Unique’ is defined as specific to an assembly (mm9 or mm10). Significance is defined as a q-value below or equal to 0.05. ‘Overlapping’ is defined as common between mm9 and mm10 reanalyses. ‘Almost overlapping’ is defined as common between mm9 and mm10 at a threshold of 0.1 but not as the 0.05 threshold.

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