. 2024 May 7;25:116. doi: 10.1186/s13059-024-03253-3

Table 2.

SV-related DEGs in AS and EU ancestral group pairwise comparison

SV	Specific or high F_ST	Gene name	Event type	Tssue	logFC	Bonferroni P
1:119154722–119155024:DEL	Highest F_ST	MYO5A	3′-UTR DEL (MEI)	Embryo	3.15	4.66E−12
				Heart	− 1.22	3.44E−03
				Skin	1.31	3.29E−03
				Uterus	2.13	1.13E−08
10:65581173–65581438:MEI	AS specific	AKR1C2	5′-UTR DEL (MEI)	Liver	− 1.72	4.38E−18
			pLoF (St)
			Promoter DEL (MEI)
			5′-UTR DEL (MEI)	Uterus	5.01	8.93E−27
			pLoF (St)	Uterus	5.01	8.93E−27
11:22010860–22011147:MEI	AS specific	GTF2F2	3′-UTR DEL (MEI)	Embryo	4.06	3.25E−21
				Liver	− 2.06	1.09E−20
				Skin	1.38	1.35E−03
12:23080412–23096524:DUP	AS specific	PLXDC1	CpGn (Wk)	Adipose	− 1.59	1.88E−11
			Enhancer DUP	Adipose	− 1.59	1.88E−11
			CpGn (Wk)	Skin	− 1.41	3.67E−04
13:138175850–138229580:DUP	AS specific	CCDC58	CpGn (St)	Embryo	3.17	2.70E−12
				Skin	1.96	9.79E−09
				Uterus	2.28	1.63E−08
16:32285866–32287949:DEL	AS specific	ITGA1	pLoF (Wk)	Liver	− 1.15	7.65E−05
				Muscle	− 1.48	3.27E−04
				Uterus	−1.26	1.58E−03
3:68099167–68099419:MEI	AS specific	POLE4	3′-UTR DEL (MEI)	Embryo	4.53	3.71E−26
3:68099167–68099419:MEI	AS specific	POLE4	3′-UTR DEL (MEI)	Uterus	1.49	3.13E−03
4:2689951–2695878:DEL	AS specific	PTK2	pLoF (Wk)	Embryo	3.30	1.75E−11
			Enhancer DEL (MEI)	Liver	− 1.22	2.11E−04
			pLoF (Wk)	Liver	− 1.22	2.11E−04
			pLoF (Wk)	Skin	1.58	2.11E−05
6:169060140–169064984:DEL	AS specific	FOXJ3	3′-UTR DEL (MEI)	Embryo	4.27	5.39E−24
				Liver	− 1.27	1.72E−03
				Uterus	1.49	3.31E−03
8:77217828–77233717:DUP	AS specific	GATB	5′-UTR DUP	Liver	− 1.30	8.83E−03
			Enhancer DUP	Liver	− 1.30	8.83E−03
			5′-UTR DUP	Uterus	2.13	1.67E−05
5:77968631–77972413:DEL	EU specific	RPAP3	pLoF (Wk)	Embryo	2.50	1.99E−06
5:77968631–77972413:DEL	EU specific	RPAP3	pLoF (Wk)	Skin	2.15	8.93E−10
8:41223207–41783659:DUP	EU specific	KIT	eQTL DUP	Adipose	1.92	4.53E−12
			WlGnDup	Adipose	1.92	4.53E−12
			WlGnDup	Skin	1.68	1.40E−06