Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs

Zhang, Xiaoling; Gierman, Hinco J; Levy, Daniel; Plump, Andrew; Dobrin, Radu; Goring, Harald HH; Curran, Joanne E; Johnson, Matthew P; Blangero, John; Kim, Stuart K; O’Donnell, Christopher J; Emilsson, Valur; Johnson, Andrew D

doi:10.1186/1471-2164-15-532

BMC Genomics

Table 3 trans -eQTLs (>500 kb) observed in 4 or more datasets

From: Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs

Chr	Pos (Mb)	Nearby gene(s) [#datasets], fxn*	trans eQTL(s)^†	eGene targets‡	eGene (distances)
1	143	NBPF ncRNAs [12], intron	rs10907360	Many targets	0.65-3.6 Mb
1	201	PPP1R12B[4], nSNP, splice site^a	rs3881953,rs12734338,rs12743401	Many targets	other chr.
2	60	BCL11A[4], intron^b	rs766432	HBG1[4], HBG2[3]	other chr.
3	100	CPOX[4]	rs1461161,rs1675511	DCAF12L1[4]	other chr.
3	40	ENTPD3[5], intron	rs2371185	Many targets	other chr.
3	40	ENTPD3, EIF1B[4]	rs2123999,rs11717036	Many targets	other chr.
3	40	ENTPD3, RPL14[4],3′UTR, intron	rs9848083,rs4973898,rs11539046	Many targets	other chr.
3	42	ULK4[9], nSNP^c	rs1052501,rs10212536,rs3934103	CTNNB1[9]	0.55-0.7 Mb
5	0.3	SDHA[4], intron	rs6869925,rs6878087	SDHAP3[4], KRT6B[1]	other chr + cis
5	2	SDHAP3[4], intron, near TSS	rs7734561	CEP72[1], PDCD6[3]	0.94-1.3 Mb
6	164	PACRG[9], 3′UTR	rs9306	PARK2[9]	0.58 Mb
6	31	MHC locus [6]^d	rs6457374,rs2247056	Many targets	other chr + cis
6	31	MHC locus [4]^d	rs2074488	Many targets	other chr + cis
6	33	MHC locus [7]^d	rs2395185,rs9268853,rs9268858, +1 other	Many targets	other chr.
7	74	GTF2I[4], intron	rs13238568	GTF2IP1[4]	0.52 Mb
10	48	ZNF488[4]	rs4342964	ANXA8L2[3], RP11-144G6.7[1]	0.71-0.95 Mb
11	0.8	RPLP2[4], intron	rs10902222	LRFN1[3], HCN2[1], FAM72B[1]	other chr.
11	55	TRIM48[6]	rs10792252	SPRYD5[6]	0.78 Mb
12	55	SUOX, IKZF4[5]^e	rs10876864	Many targets	other chr.
16	68	NFAT5[4], intron	rs1064825	AARS[4]	0.56 Mb
17	34	MRPL45[4]	rs4329955,rs4514720	TBC1D3B/C/G[4]	1.8-2.2 Mb
17	40	ENSG00000214447,CCDC103[4], 5′UTR	rs2277616	ITGA2B[4]	0.51 Mb
17	41	MAPT[11], intron^f	rs17651507,rs3785885,rs8079215	ARL17A[5], ARL17P1[6], LRRC37A2[5]	0.52-0.57 Mb
17	41	CRHR1[7], intron	rs12150547,rs2696425,rs418891, +46 others	Many targets	other chr.
17	41	MAPT[7], intron	rs1864325,rs17762165,rs17688922, +62 others	Many targets	other chr.
17	42	MAPT,NSF[7], synonymous, intron	rs199535,rs169201,rs199448, +2 others	Many targets	other chr.
17	42	MAPT,KIAA1267[4], intron	rs2532332,rs17659881,rs17660065, +6 others	Many targets	other chr.
17	42	MAPT,KIAA1267[4], intron	rs17660595,rs17563986,rs17649553, +53 others	Many targets	other chr.
19	22	BC033373, ZNF99, ZNF486 + 6 other ZNFs [4], UTR	rs3817397,rs8112960,rs7254018	ZNF595[4], ZNF479[2], ZNF679[2], ZNF486[1], ZNF99[1]	other chr.
22	20	PI4KA, CRKL[4], intron	rs178058,rs5761386,rs4822700	PI4KAP2[3], POM121L10P[1]	0.63-3.8 Mb

*Representative nearby genes are given. Number of datasets with ≥1 target eGene originating from this trans-eQTL locus are given in brackets. Functional annotation of trans eSNPs are given. †trans eSNPs were grouped within blocks of perfect linkage disequilibrium (r² = 1). ‡Where there were limited targets the target eGenes are given with the number of datasets for each in brackets. For all loci including those with Many targets more detailed association information is found in Additional file 8. Results from the GRASP GWAS database for SNPs or those in perfect LD (r² = 1): ^aasthma (P < 2E-6), ^bfetal hemoglobin (P < 2E-20), beta-thalassemia severity (P < 1E-10), ^cblood pressure (P < 2E-7), multiple myeloma (P < 8E-9), ^dmany pleiotropic associations, ^etype I diabetes (P < 2E-16), alopecia areata (P < 9E-8), adult asthma (P < 3E-6), ^fprogressive supranuclear palsy (P < 2E-120), Parkinson’s disease (P < 2E-16), primary biliary cirrhosis (P < 6E-6).

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ISSN: 1471-2164

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