CNSD 3.5 Interpreting non-coding DNA variants with genomic data

What are expression quantitative trait loci (EQTLs)?

Genomic loci that explain variation in expression levels of mRNAs. There is a link between variations and genetic polymorphisms. It shows the gene expression of a certain gene. You can then look if a certain mutation causes a certain altered gene expression.

Analyse the graph with ATACseq data.

• X-axis = the place on the genome/chromosome

• Y-axis = the strength of the ATAC signal (when there is a peak on the Y-axis, it means that the DNA was more open and suggests activity)

• A = enhancer, localized in an intron

• B = promotor, the start of the gene

• C = enhancer, open DNA, but not on the same place as the promotor

• D = closed chromatide, there is no signal

• The arrows show the introns, a block is the start of a gene, and the arrows show the reading direction.

What gene is a marker for microglia?

CX3CR1

What is meant with a causal SNP?

The exact variant that can cause the disease. When it is not located in ATAC, it is not a causal SNP. This regio is then closed and does thus not function.

What is the difference between eQTL and ATAC?

eQTL confirms the correlation with gene expression, whereas ATAC confirms localization to putative regulatory elements.