In this gist I'm collecting all those 'crazy' bash snippets that might be useful in the future, or have some other reason to get remember of.

bioinfo.sh

# Get overlapping protein-coding genes for a set of rsIDs:
variants="rs6796106
rs191957455
rs41264153
rs145265828"

# This script loops through a set of variants and returns the overlapping gene(s):
for v in $variants ; do wget -q http://ec2-54-91-140-228.compute-1.amazonaws.com:5000/variation/human/${v}.json -O - | jq -r '"\(.name) \(.mappings[0].location)"'; done | while read rsID location; do genes=$(wget -q "http://ec2-54-91-140-228.compute-1.amazonaws.com:5000/overlap/region/human/${location}?feature=gene&content-type=application/json" -O - | jq -r '[ .[] | select(.biotype == "protein_coding").external_name ] | join(",")') ; echo $rsID $genes; done

# This script looks up a variant in the eQTL database (through the Ensembl REST API), and returns all the genes in which the p-value was lower than1e-9 (Also returns the gene names as well from a separate REST query)
variant="rs2736340"
cat  <(echo "GeneName GeneID Cell_type -log(pvalue)") <(wget -q "http://ec2-54-91-140-228.compute-1.amazonaws.com:5000/eqtl/variant_name/homo_sapiens/${variant}?content-type=application/json;statistic=p-value" -O - | jq -r '.[] | select ( .minus_log10_p_value > 9) | "\(.gene) \(.tissue) \(.minus_log10_p_value)"' | sort -k3,3nr| while read geneID tissue pval; do gene_name=$(wget -q --header='Content-type:application/json' "http://ec2-54-91-140-228.compute-1.amazonaws.com:5000/lookup/id/${geneID}" -O - | jq -r '.display_name'); echo ${gene_name:--} $geneID $tissue $pval;done)  | column -t