Astrazeneca Phewas analysis using the UK biobank

[Nightsong]

On the chromatin regulator KMT5B and its links to autism, a few papers -

Pleiotropy of autism-associated chromatin regulators

Autism risk gene KMT5B deficiency in prefrontal cortex induces synaptic dysfunction and social deficits via alterations of DNA repair and gene transcription

Autism genes converge on asynchronous development of shared neuron classes

KMT5B is required for early motor development

Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders

Multiple autism genes influence GABA neuron remodeling via distinct developmental trajectories

 

[hotblack]

DecodeME LocusZoom for BTN2A1 and genecard (this is the one in an area of a hit, you can see how it could be a promotors/enhancers of this gene like this one shown on Genehancer and LocusZoom although there seems to be lots of uncertainty and the SNPs could modify genes a long way away)

I’ll run my promoters/enhancers scripts on the top genes mentioned here to help us prod around.

 

[hotblack]

Here you go, should allow easy access to the genecard for each gene and the genehancer info, ensembl info, locuszoom etc for the regulatory elements

Index of AstrazenecaPE

So here’s all the decodeme identified snps in the area whch pass the significance threshold and could be promoters or enhancers for BTN2A1 according to genehancer info.

Picking the top one you can quickly see the location on locuszoom.
And clicking on the GHID takes you to the genehancer info where you can see that the potential gene targets, which include a novel transcript at the top but also interestingly other DecodeME genes like ABT1, ZNF322, H4C8 and BTN2A2 as possible targets.

Which is to say, it’s complicated. There’s probably a better way of working out all this than my janky scripts (buyer beware). I suspect it’s the sort of thing some bioinformatics pipeline does, but hopefully this is useful for others to prod around