Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies

Joehanes, Roby; Zhang, Xiaoling; Huan, Tianxiao; Yao, Chen; Ying, Sai-xia; Nguyen, Quang Tri; Demirkale, Cumhur Yusuf; Feolo, Michael L.; Sharopova, Nataliya R.; Sturcke, Anne; Schäffer, Alejandro A.; Heard-Costa, Nancy; Chen, Han; Liu, Po-ching; Wang, Richard; Woodhouse, Kimberly A.; Tanriverdi, Kahraman; Freedman, Jane E.; Raghavachari, Nalini; Dupuis, Josée; Johnson, Andrew D.; O’Donnell, Christopher J.; Levy, Daniel; Munson, Peter J.

doi:10.1186/s13059-016-1142-6

Table 4 Top 25 non-redundant gene level cis-eQTL and top 25 trans-eQTL-transcript cluster pairs

From: Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies

eQTL marker position	Rs ID	Transcript cluster ID	Trans Chr	Gene symbol	R²	Beta	Cluster number
Top Cis-eQTL pairs
12:10118747	rs12231872	3404530 R	12	CLEC12A	57%	−0.15 [G]
15:48596713	rs74011998 G	3593065	15	SLC12A1	56%	−0.15 [T]
5:96252589	rs2910686 H G	2821347 R	5	ERAP2	55%	−0.11 [T]
1:207280764	rs12063500 G	2377165 R	1	C4BPA	54%	−0.32 [C]
6:31238135	rs1050317 G	2948887	6		50%	−0.3 [A]
6:32576341	rs9271093 G	4048241 R	6	HLA-DRB5	50%	−0.45 [A]
22:42498204	rs12157818	3947310 R	22	C22orf32	49%	0.16 [C]
6:26354100	rs67509210 G	2899333 R	6	BTN3A2	48%	0.19 [G]
7:150480007	rs1985881	3079172 R	7	TMEM176B	48%	−0.17 [C]
4:6697822	rs3822260 H G	2717078	4	S100P	48%	0.24 [C]
22:45744854	rs8136319	3948543 R	22	FAM118A	48%	−0.2 [G]
6:167382449	rs434093 G	2984884 R	6	RNASET2	48%	0.12 [T]	21
1:17421764	rs2076613	2398820	1	PADI2	47%	0.08 [T]
X:109206541	rs2499412	3987029	X	TMEM164	47%	0.11 [G]
4:47858518:ATAG_		2768273	4	NFXL1	47%	−0.1 [R]
5:64858687	rs432206 H	2859667 R	5	CENPK	47%	−0.14 [C]
7:150478052	rs6464101 H	3031624 R	7	TMEM176A	47%	−0.15 [G]
1:109706880	rs647294 H	2350489 R	1	KIAA1324	47%	0.14 [G]
6:32575544	rs9271061 G	4048265 R	6	HLA-DRB1	46%	−0.55 [T]
5:102118794	rs2431321 H	2822215 R	5	PAM	46%	−0.08 [T]
6:32603854	rs9272302 G	2903219 R	6	HLA-DRB6	46%	−0.77 [C]
7:26952139	rs2960785 H	3042610 R	7	SKAP2	46%	0.08 [C]
1:43265985	rs2816599	2409069 R	1	CCDC23	45%	−0.31 [C]
9:132588337	rs7470675	3227121 S	9	C9orf78	45%	0.17 [T]
7:75247329	rs1186222	3057370 R	7	HIP1	45%	0.09 [C]
Top Trans-eQTL Pairs
7:50427982	rs6592965 G	4007437 R	X	SLC38A5	22%	0.09 [G]	25
17:44026739	rs242562 H G	3767230	17	LRRC37A3	20%	0.16 [G]
3:30722412	rs3773654	3638566	15	PEX11A	16%	–0.18 [G]
1:58992071	rs7520008	2414558	1	DAB1	12%	0.04 [T]
3:50078541	rs9814664 H G	3981931	X	ZCCHC13	12%	0.11 [T]	9
7:50427982	rs6592965 G	2520069 R	2	C2orf88	11%	0.1 [G]	25
1:248039451	rs3811444 H G	3357237 R	11	JAM3	11%	0.08 [C]	4
3:49978069	rs6772095 H G	4024310	X	SOX3	11%	0.06 [C]	9
16:69973655	rs4985461	2876543	5	TIFAB	11%	–0.08 [G]
7:50427982	rs6592965 G	3724505	17	MYL4	9%	0.08 [G]	25
21:44473062	rs11700748 H G	3416019	12	PRR13	9%	0.1 [C]	56
5:50106439	rs32396 H G	2359431	1	LCE1F	8%	0.08 [G]
11:617537	rs2740380 G	3864107	19	PSG7	8%	0.13 [T]
3:49971514	rs7613875 H G	3693591	16	PRSS54	8%	0.06 [C]	9
3:50008566	rs6446189 G	3939154	22	RAB36	8%	0.05 [A]	9
3:56849749	rs1354034 H G	3724545 R	17	ITGB3	8%	–0.08 [T]	10
11:108623805:CTAT_		3504617	13	SKA3	8%	–0.1 [R]
17:33875262	rs8073060 H	3089102 R	8	EPB49	7%	–0.05 [T]	51
3:56849749	rs1354034 H G	2735759	4	MMRN1	7%	–0.07 [T]	10
11:55113534	rs75905900 G	3329983	11	PTPRJ	7%	–0.05 [A]
6:170847101	rs75159687	2390976	1	LINC00115	7%	–0.13 [T]
22:50027210	rs5769712	3581090	14	TMEM179	7%	0.06 [C]	58
7:50427982	rs6592965 G	3714729 R	17	MAP2K3	7%	–0.05 [G]	25
22:50027210	rs5769712	3203199	9	TAF1L	6%	0.07 [C]	58
3:56849749	rs1354034 H G	2476510	2	LTBP1	6%	–0.06 [T]	10

R² - Percentage variance explained
Marker position is annotated as chromosome number:location in hg19 coordinate
Beta is regression estimate (log base 2 expression difference per dosage of effect allele), with effect allele in brackets. [R] refers to the reference allele for an indel polymorphism
H = HapMap SNPs
G = in LD with GWAS SNPs as recorded in the NHGRI GWAS catalog
R = In LD with SNP replicated in at least one of the databases associated with references GTEx [1], Westra et al. [5], Liang et al. [6], Kirsten et al. [8]
All 25 cis-eQLTs and 25 trans-eQLTs are internally validated and have consistent sign of expression change
S = SNP-in-probe problem likely inflates R²

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ISSN: 1474-760X

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