A table containing all trait-associated SNPs with P<10−8 was downloaded from the NCBI dbGaP Association Results Browser (3,781 total trait-associated SNPs). Genomic coordinates of trait-associated SNPs were retrieved from dbSNP 130. To compare enrichment of trait-associated SNPs in lincRNAs versus background loci (nonexpressed intergenic regions), regions of the uniquely mappable genome longer than 200 bp that exclude all evidence of transcription (RNA-seq reads, RefSeq NM, NR and XR genes and pseudogenes, Ensembl v61 genes, GENCODE v10 genes, spliced ESTs, spliced H-Invitational cDNAs, 5′ and 3′ UTRs from UTRdb, extended RefSeq NM genes derived using reference annotation based de novo transcriptome assembly (see above and Dataset S1) and all lincRNAs) were compiled and served as background loci for this analysis. The number of tested SNPs on Illumina (Illumina 1M) and Affymetrix (Affymetrix SNP Array 6.0) SNP arrays was determined for RefSeq NM gene exons, lincRNA exons and background loci. The number of tested SNPs per platform was scaled by the fractional contribution of Illumina (58.6%) versus Affymetrix (41.4%) platforms to the full set of GWASs in the NHGRI GWAS catalog [1].
