Supplementary Figure Legends
Figure S1. (a) The average SNP density of lincRNAs with different numbers of
annotated exons. Error bars are mean ± s.e.m. (b) Number of ECRs identified in human
lincRNAs used different threshold criteria for the size and identity.
Figure S2. A representative example of disease-associated SNPs in low SNP density
lincRNA. Top: The SNP density in lincRNA region (black), flanking regions and
neighboring
protein-coding
genes
(grey).
Bottom:
magnified
view
of
the
disease-associated SNPs (green) and other SNPs (red) in the lincRNA region (blue box).
Figure S3. Functional enrichment analysis of the nearest genes to lincRNAs. (a) The
average SNP density of the top 5% low/high SNP density lincRNAs. (b) GO enrichment
analysis results. Red bars represent the top hits for the nearest genes of the top 5% low
SNP density lincRNAs. Grey bars represent the top hits for the nearest genes of the top
5% high SNP density lincRNAs. (c) The average percent of ECR length in top 5%
highly/poorly conserved lincRNAs. (d) GO enrichment analysis results. Red bars
represent the top hits for the nearest genes of the top 5% highly conserved lincRNAs.
Grey bars represent the top hits for the nearest genes of top 5% poorly conserved
lincRNAs. All the enrichment P-values were calculated using DAVID.
Figure S4. Functional enrichment analysis of lincRNAs. (a) The average SNP density
of the top 100 low/high SNP density lincRNAs. (b) GO enrichment analysis results. Red
bars represent the top hits for top 100 low SNP density lincRNAs. Grey bars represent
the top hits for the top 100 high SNP density lincRNAs. (c) The average percent of ECR
length in the top 100 highly/ poorly conserved lincRNAs. (d) GO enrichment analysis
results. Red bars represent the top hits for the top 100 highly conserved lincRNAs. Grey
bars represent the top hits for the top 100 poorly conserved lincRNAs. All the
enrichment P-values were calculated using DAVID.
Figure S5. A representative example of disease-associated SNP having a large effect on
predicted lincRNA secondary structure. Top: SNP density in lincRNA (black), flanking
regions and neighboring protein-coding genes (grey). Bottom: the disease-associated
SNPs (green) in the lincRNA region (blue box) and ECR region (blue block). The MFEs
and RNA secondary structures for the wild-type and mutant sequences were predicted
by RNAfold.