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Visualising a genomic region in human

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Visualising a genomic region in human

Go to Ensembl Beta.

  1. Navigate to the region from 176,092,720 to 176,190,907 on the human GRCh38 assembly on chromosome 2. This region contains the HOXD gene cluster.
    • How many HOXD genes can you find in this region?
    • On a new browser tab, search for the gene cluster in GeneCards. What diseases are associated with the gene cluster? (Hint: you can search for gene clusters by adding an ‘@’ sign to the gene name, i.e. HOXD@).
  2. Navigate to the HOXD1 gene. Let’s explore any overlapping regulatory features.
    • Does this gene overlap any regulatory features? What type of regulatory element is this/are they?
    • Downstream of the regulatory feature, should see a neighbouring regulatory element in the colour purple. What is this regulatory feature? How does it differ from an enhancer or promoter?
  3. Let’s explore variants found within the HOXD1 gene.
    • What groups of variants can you find in the HOXD1 region?
    • Zoom in on the first yellow-coloured variant. What type of variant is this and what are the alleles?
    • What is the source of the variant? Can you provide the variant location in Variant Call Format (VCF)?
  1. In the Genome Browser app, click on the Navigate browser image icon in the track panel on the right. Expand Go to new location, select Chr 2, enter 176,092,720 in Start and 176,190,907 in End. Click on the green Go button. Count the number of HOXD genes in the genome browser on the left.

    There are 9 HOXD genes on the forward and 1 HOXD gene on the reverse strand in this region.

    Go to the GeneCards entry for the HOXD cluster. You can find diseases associate with the cluster in the Summaries for HOXD@ Gene section.

    • The HOXD gene cluster is associated with synpolydactyly and clubfoot.
  2. In the genome browser, click on the HOXD1 (ENSG00000128645.15) gene and select Genome Browser in the pop-up menu. Scroll down to find the Regulatory track, which is indicated with the letter R on the far left. Click on the regulatory feature to see what type it is. Alternatively, you can find a legend in the track panel under the Regulation tab on the right.

    The gene overlaps 1 regulatory feature: the promoter ENSR00000629037.

    In the Regulation (R) track in the genome browser, click on the purple regulatory feature. The pop-up menu will tell you what type of regulatory feature this is. To find a description of the feature, go to the Regulation tab in the track panel on the right. Click on the three dots (…) next to TF binding.

    • This regulatory feature is a TF binding site. These are sites that are enriched for Transcription Factor (TF) binding, but they lack epigenomic evidence to be classified as an enhancer or promoter
  3. In the genome browser, scroll down to the Variation (V) track. In the track, you should see green, yellow and salmon coloured variants. You can find a colour legend in the Variation tab in the track panel on the right.

    The HOXD1 region overlaps various transcript, splicing and protein altering variants.

    Using your mouse, zoom in on the first yellow-coloured variant. Click on the first yellow variant to find out more information about it.

    • This variant (rs1691721387) is a single nucleotide variant (SNV). The reference allele is C and the alternative allele is T.

    In the pop-up menu, select View in Entity Viewer to find out more information about the particular variant. In the track panel on the right, you can find the source of the variant (at the top) and the variant location in VCF (at the bottom).

    • This rs1691721387 variant was imported from dbSNP (release 156). The VCF is as follows: 2 176188810 rs1691721387 C T.