1. What is PancanQTL?

2. Database construction pipeline.

3. Data summary.

4. The eQTL boxplot and survival Kaplan-Meier plot.

5. The identification of GWAS-related eQTLs.

PancanQTL is a database to provide a comprehensive resource of expression quantitative loci (eQTLs) across 33 human cancer types.

In PancanQTL, users can:

Browse or search cis-eQTLs and trans-eQTLs across different cancer types;

Browse or search eQTLs associated with patient survival across different cancer types;

Browse or search eQTLs in GWAS linkage disequilibrium (LD) regions;

Cancer type	Full name	No. of samples	No. of genes	No. of genotypes	Cis-pairs	Cis-egenes	Cis-eQTLs	Trans-pairs	Trans-egenes	Trans-eQTLs
ACC	Adrenocortical carcinoma	77	17562	3678145	4610	222	4558	984	60	957
BLCA	Bladder Urothelial Carcinoma	408	18171	4242910	142562	5573	120374	9199	1575	3114
BRCA	Breast invasive carcinoma	1092	17991	2765921	438476	11859	317935	73124	6013	20466
CESC	Cervical squamous cell carcinoma and endocervical adenocarcinoma	300	17975	4367017	95702	4165	84484	2209	674	971
CHOL	Cholangiocarcinoma	36	17767	4106282	11	2	11	5011	127	4436
COAD	Colon adenocarcinoma	286	17500	4576984	164356	5048	145461	3085	373	2359
DLBC	Lymphoid Neoplasm Diffuse Large B-cell Lymphoma	48	17245	4945365	391	15	391	5	3	5
ESCA	Esophageal carcinoma	184	18372	4563674	39358	1603	36589	425	56	410
GBM	Glioblastoma Multiforme	150	17650	4660522	59788	1901	55855	481	55	465
HNSC	Head and Neck squamous cell carcinoma	518	17985	4302347	267797	6502	228069	9285	1064	7389
KICH	Kidney Chromophobe	66	17212	3902792	7264	320	7038	5826	157	4669
KIRC	Kidney renal clear cell carcinoma	527	17812	4632879	521072	8739	410720	13978	943	12200
KIRP	Kidney renal papillary cell carcinoma	290	17715	4981141	186310	4920	164159	2712	302	2516
LAML	Acute Myeloid Leukemia	123	17099	5245402	70375	1758	64696	580	38	397
LGG	Lower Grade Glioma	515	17563	4688205	578617	9177	437580	21236	1804	13084
LIHC	Liver hepatocellular carcinoma	369	17816	4218042	151613	5723	128956	16675	2230	3963
LUAD	Lung adenocarcinoma	514	18190	4435432	259475	6834	220709	6157	745	4513
LUSC	Lung squamous cell carcinoma	500	18277	3787605	204145	6367	173856	11934	1050	10487
MESO	Mesothelioma	87	17742	4904165	16527	475	16140	474	43	471
OV	Ovarian serous cystadenocarcinoma	301	18137	3018011	92743	7100	74419	6196	2028	2245
PAAD	Pancreatic adenocarcinoma	178	18021	5099858	113810	2468	104058	1221	110	978
PCPG	Pheochromocytoma and Paraganglioma	178	17552	4836419	93679	3203	83517	1146	241	985
PRAD	Prostate adenocarcinoma	494	17646	4887130	691299	10152	514457	15730	1105	11589
READ	Rectum adenocarcinoma	94	17427	4653098	22788	781	22114	72	14	72
SARC	Sarcoma	258	18183	4156361	70201	4194	61193	5704	1055	4115
SKCM	Skin Cutaneous Melanoma	103	17645	4968336	15046	720	14487	348	45	299
STAD	Stomach adenocarcinoma	415	18478	4362659	161271	4913	142709	2470	391	1994
TGCT	Testicular Germ Cell Tumors	150	18790	4927197	71832	1959	67882	653	39	599
THCA	Thyroid carcinoma	503	17277	4936390	927678	10766	659323	13592	745	8908
THYM	Thymoma	120	17785	5036992	85627	2090	78507	436	43	379
UCEC	Uterine Corpus Endometrial Carcinoma	176	18195	5111002	25426	1188	24721	251	35	248
UCS	Uterine Carcinosarcoma	56	18314	4036518	488	25	488	6	2	6
UVM	Uveal Melanoma	80	16758	4812283	26233	890	25260	5	4	5

eQTL boxplot	Kaplan-Meier plot
Boxplots represent the gene expression in individuals carrying homozygote AA, heterozygous Aa, and homozygote aa, respectively.	Lines represent the survival curve for individuals carrying homozygote AA, heterozygous rs1824937 Aa, and homozygote aa, respectively.

GWAS tagSNPs were downloaded from GWAS catalog website (http://www.ebi.ac.uk/gwas/) and the GWAS linkage disequilibrium regions were extracted from SNAP database (https://archive.broadinstitute.org/mpg/snap/ldsearchpw.php). eQTLs that overlapp with tagSNPs and/or linkage disequilibrium regions were extracted as GWAS-related eQTLs.