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Online Table List

Table S1	The TCGA specimens analyzed in the present study
Table S2	The gene annotation (GENCODE V18) used in the present study
Table S3	The number of the detectable lncRNAs in each cancer type
Table S4	The list of lncRNAs whose expression were detected in all 13 cancer types
Table S5	The list of lncRNAs whose expressions were detected in at least one cancer type
Table S6	The list of detectable lncRNAs in each cancer type
Table S7	The list of dysregulated lncRNAs in BRCA
Table S8	The list of dysregulated lncRNAs in COAD
Table S9	The list of dysregulated lncRNAs in HNSC
Table S10	The list of dysregulated lncRNAs in KIRC
Table S11	The list of dysregulated lncRNAs in LUAD
Table S12	The list of dysregulated lncRNAs in LUSC
Table S13	The list of dysregulated lncRNAs in PRAD
Table S14	The list of lncRNAs whose up-regulations are shared among different cancer types
Table S15	The list of lncRNAs whose down-regulations are shared among different cancer types
Table S16	The list of lncRNAs whose up-regulations are unique among different cancer types
Table S17	The list of lncRNAs whose down-regulations are unique among different cancer types
Table S18	Percentages of lncRNAs with significant copy number alteration (>25% of specimens) in each cancer type
Table S19	The list of lncRNAs located in the focal alteration loci in BLCA
Table S20	The list of lncRNAs located in the focal alteration loci in BRCA
Table S21	The list of lncRNAs located in the focal alteration loci in COAD
Table S22	The list of lncRNAs located in the focal alteration loci in GBM
Table S23	The list of lncRNAs located in the focal alteration loci in HNSC
Table S24	The list of lncRNAs located in the focal alteration loci in KIRC
Table S25	The list of lncRNAs located in the focal alteration loci in LAML
Table S26	The list of lncRNAs located in the focal alteration loci in LUAD
Table S27	The list of lncRNAs located in the focal alteration loci in LUSC
Table S28	The list of lncRNAs located in the focal alteration loci in OV
Table S29	The list of lncRNAs located in the focal alteration loci in PRAD
Table S30	The list of lncRNAs located in the focal alteration loci in SKCM
Table S31	The list of lncRNAs located in the focal alteration loci in UCEC
Table S32	The probes corresponding to the promoter regions of lncRNA genes
Table S33	The list of CAESLG candidates of each cancer type
Table S34	The cancer-associated SNPs reported by the NHGRI Catalog of Published GWAS Catalog database
Table S35	The list of index SNPs located in genomic loci harboring lncRNA genes
Table S36	The list of index SNPs located in genomic loci harboring lncRNA genes in each cancer type