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 LD/CCV SNP's GWAS SNP location. The blue line corresponds to the average copy number of ER-positive normal samples, while the red line corresponds to that of the corresponding tumor samples.
Data source: TCGA-BRCA copy number segmentation.

Credible causal variant (CCV):

Below, we show whether the queried LD SNP is in the list of credible causal variants from the study by Fachal et al..

Is {{ ldSNP }} a CCV? {{ isCCV }}

High confidence target genes for {{ ldSNP }}: {{ genes }}

The figure below shows prediction of contact counts in MCF-7 (based on Hi-C data) as a function of distance centered around the SNP of interest. Predictions are made in 5 kb bins, spanning ± 1 Mb around the SNP location (vertical line). A total of 10 different models are used to predict the counts in MCF-7; the plot below shows the average of counts across the 10 models. The predictions for which at least one model shows significance (q < 0.05) is filled in red. The size of the markers is proportional to the number of models showing significance. The gene names in the interacting bins for which there is more than one model showing significance are also displayed wherever applicable.

Significant results:

Data source: TCGA-BRCA genotypes and gene expression data

{{ name }}
{{ col }} {{ col }}

Select target gene:

(Submit above) is the homozygous risk genotype group. The eQTL results are displayed for the queried GWAS SNP. The normalized expression refers to the residuals after regressing out copy number.

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: Breast tissue/breast cancer only All

{{ name }}
{{ col }} {{ col }}

Page = {{ currentPage }} of {{ totalPages }}

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. One can also click the button in the motif logo column to display the motif of the corresponding TF. Currently, motif logos are shown for top 10 motifs. 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 JASPAR, HOCOMOCOv10, ENCODE, SwissRegulon, TRANSFAC, Jolma2013 and FactorBook databases

{{ name }}	motifLogo
{{ col }}

Page = {{ currentPage }} of {{ totalPages }}

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-BRCA gene expression data

GWAS SNP

LD SNP

CCV SNP

Annotation (GWAS Catalog)

Copy number:

Credible causal variant (CCV):

Is {{ ldSNP }} a CCV? {{ isCCV }}

High confidence target genes for {{ ldSNP }}: {{ genes }}

Significant results:

Select target gene:

Motif disruption:

Putative transcription factor-target gene expression correlation:

Select target gene: