Tracks are obtained from the following databases: ENCODE, WashU browser and ReMap 2018.

Copy number:

The figure below shows the normalized copy number [log₂(copy_number/2)] at the selected GWAS SNP location. The blue line denotes the average copy number of all normal samples, while the red line denotes the average copy number of the corresponding tumor samples.
Data source: TCGA-LGG copy number segmentation.

Select a molecular group:

Significant results:

Data source: TCGA-LGG genotypes and gene expression data

Note: "Other groups combined" = non-"IDH-mutant only" and non-"Triple-Positive" samples.

Select a molecular group:

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Select target gene:

(Submit above) is the homozygous risk genotype group. The eQTL results are displayed for the queried LD SNP.

The table below shows all ChIP-seq peaks from ENCODE covering the queried LD SNP location. The ENCODE_ID links to the corresponding experiment page on the ENCODE website.
Data source: ChIP-seq peaks from ENCODE

Search:

Cell lines: Brain tissue/cell line only All

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Motif analysis
Expression correlation

Motif disruption:

The table below shows a list of candidate transcription factors (TFs) whose binding affinity was significantly disrupted by the queried LD SNP. Column permPvalue displays the permutation test p-value for testing the significance of motif disruption. Note: if there are no candidate TFs from our analysis, then no results will be displayed below.
Data source: Motifs from JASPAR2016, HOCOMOCOv10, Jolma2013 and TRANSFAC databases

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Putative transcription factor-target gene expression correlation:

The columns in the heatmap are the genotype groups with the homozygous risk group highlighted in red. The rows are the putative transcription factors (TFs) from motif analysis (see the left tab). Note: if there are no candidate TFs from our analysis then no results will be displayed below.
Data source: TCGA-LGG gene expression data

Select a molecular group:

Gene locus

OR

GWAS SNP

LD SNP

Annotation (GWAS Catalog)

Copy number:

Significant results:

Select target gene:

Motif disruption:

Putative transcription factor-target gene expression correlation:

Select target gene: