Molecular Vision: Geisert, Mol Vis 2009; 15:1730-1763. Table 4

Table 4. Cis-trans gene pairs (cis=cause, trans=target).

Target transcript with trans-QTL								Causal candidate gene (cis-QTL)
Target gene		Exp Level	Affy ID	LRS	QTL Chr	QTL Range	Tissue or function	Candidate gene		Affy ID	Chr	Mb	LRS
Tyr	tyrosinase (albino c locus)	10.7	1417717*	29.6	4	78–81	pigmentation	Tyrp1	tyrosinase related protein 1 (b locus)	1415862*	4	80.3	56.2
Dct	dopachrome tautomerase	14	1418028*	20	4	60–95	retinal pigment epithelium	Tyrp1	tyrosinase related protein 1 (b locus)	1415862*	4	80.3	56.2
Asip	agouti signaling protein	6.2	1420516*	19.8	1	58–63	pigmentation	Nbeal1	neurobeachin like 1	1441444*	1	60.2	10
Mela	melanoma antigen	8.6	1433438*	131	9	74–77.5	retinal pigment epithelium	Myo5a	myosin 5a (dilute d locus)	1419754*	9	75	159
Mcam	melanoma cell adhesion molecule	7.6	1416357*	31.4	1	138–143	melanocyte and endothelial cell function	Nek7	NIMA (never in mitosis a)-related expressed kinase 7	1416816*	1	140.3	19.2
Bfsp2	phakinin	12.9	1434463*	25.6	3	143–147	lens	Col24a1	procollagen type 24 alpha 1	1453418*	3	145.5	11.3
Lenep	lens epithelial protein	11.3	1424423*	25.2	5	111–114	lens	Cryba4	crystallin beta A4	1420686*	5	112.5	24.1
Cd59a	protectin, Cd59a antigen	10.8	1418710*	48.5	13	62–69	retina, immune function	Zfp58	zinc finger protein 58	1455945*	13	68	13
Ahnak	desmoyokin	7.1	1428058*	56	5	110–114	epithelium, motility	Cryba4	crystallin beta A4	1420686*	5	112.5	24.1
Eif4g2	translation initiation factor 4, gamma 2	12.9	1415862*	39.8	4	94–97	photoreceptor function	Hook1	hook 1	1438018*	4	95.5	18.1
Cks1b	CDC28 protein kinase 1b	8.6	1448441*	39.1	1	193–195	unknown, not retina	Rd3	retinal degeneration 3	1452355*	1	193.7	23.6
Ptp4a1	PRL1 cone phosphatase	11.5	1449322*	42	5	111–115	retinal function	Kctd10	potassium channel tetramerisation domain 10	1423694*	5	114.6	20
Ctnna1	catenin alpha 1	12.3	1448149*	20.5	14	9.5–18.5	unknown, possible retinal function	Atxn7	ataxin 7 (photoreceptor degeneration)	1442186*	14	12.9	48.1
Pten	phosphatase and tensin homolog	11.6	1422553*	21	5	136–139	unknown, possible retinal function	Zpf68	zinc finger protein 68	1457462*	5	138.8	64.5
Ldhb	lactate dehydrogenase 2, B chain	12.4	416183*	17	8	14–17	retinal ganglion cell function	Dlgap2	PSD-95/SAP90-binding protein 2	1457979*	8	14.9	14
Nars	asparaginyl-tRNA synthetase	11.9	1452866*	39	1	174–178	neuronal function	Fmn2	formin 2	1450063*	1	176.7	20.5
Pacsin3	protein kinase C and casein kinase substrate in neurons 3	10.6	1437834*	34.9	3	144.5–147	neuronal function	Sh3glb1	SH3-domain GRB2-like B1 (endophilin)	1418012*	3	144.6	22.8
Matr3	matrin 3	8.9	1436796*	61	11	28–34	cytoskeleton	Ccdc88a	girdin (hook-related protein 1)	1436025*	11	29.4	17.3
Ifit1	interferon-induced tetratricopeptide repeats 1	8.7	1450783*	33	2	62–65	ocular immune function	Ifih1	interferon induced with helicase C domain 1	1426276*	2	62.4	40.3
Psat1	phosphoserine aminotransferase 1	10.4	1454607*	35.5	8	32.0–37.5	unknown, possible retinal function	Ppp2cb	protein phosphatase 2a, catalytic, beta	1421823*	8	35	21.6
Ube2i	ubiquitin-conjugating enzyme E2I	11.3	1422712*	32	18	23.5–34	unknown	Stard4	StAR-related lipid transfer (START) domain containing 4	1429239*	18	33.3	27.3
Hspbap1	HSPB associated protein 1	8.1	1441900*	30.7	3	141–146	lens and neuronal function	Unc5c	Unc-5c, netrin 1 receptor	1449522*	3	141.4	10
Myoc	myocilin	10.8	1450468*	21.8	2	35–41	glaucoma	Gsn	gelsolin	1456312*	2	35.1	None
Ninj1	ninjurin 1	11.6	1438928*	34.4	17	31–39	translation, oxidative stress	Cryaa	crystallin, alpha A	1452486*	17	31.4	None
Epgn	epithelial mitogen	8	1449994*	36.1	14	99–105	ocular vasculature and pigmented cells	Ednrb	endothelin receptor type B (Hirschsprung disease type 2)	1437347*	14	102.7	5