Which are the regulatory regions among the following?

Question

[Gene_MMP8]

Being from a non-bio background I am finding it hard to discover which among the following are regulatory regions and coding regions. I am interested in finding variants in regulatory regions of the genome. I have a maf file with all the regions mapped out.

[1] "3_prime_UTR_variant"
[2] "3_prime_UTR_variant,NMD_transcript_variant"
[3] "5_prime_UTR_variant"
[4] "downstream_gene_variant"
[5] "incomplete_terminal_codon_variant,coding_sequence_variant"
[6] "intergenic_variant"
[7] "intron_variant"
[8] "intron_variant,NMD_transcript_variant"
[9] "intron_variant,non_coding_transcript_variant"
[10] "mature_miRNA_variant"
[11] "missense_variant"
[12] "missense_variant,NMD_transcript_variant"
[13] "missense_variant,splice_region_variant"
[14] "non_coding_transcript_exon_variant"
[15] "regulatory_region_variant"
[16] "splice_acceptor_variant"
[17] "splice_acceptor_variant,non_coding_transcript_variant"
[18] "splice_donor_variant"
[19] "splice_donor_variant,non_coding_transcript_variant"
[20] "splice_region_variant,3_prime_UTR_variant"
[21] "splice_region_variant,5_prime_UTR_variant"
[22] "splice_region_variant,intron_variant"
[23] "splice_region_variant,intron_variant,non_coding_transcript_variant"
[24] "splice_region_variant,non_coding_transcript_exon_variant"
[25] "splice_region_variant,synonymous_variant"
[26] "start_lost"
[27] "stop_gained"
[28] "stop_gained,NMD_transcript_variant"
[29] "stop_lost"
[30] "synonymous_variant"
[31] "synonymous_variant,NMD_transcript_variant"
[32] "TF_binding_site_variant"
[33] "upstream_gene_variant"
Can someone please point to me the regulatory and coding regions among the options available above?

[Pierre Lindenbaum]

terms under http://www.sequenceontology.org/browser/current_svn/term/SO:0001566

Accession   Name    Definition  DB_Xrefs    Parents Children
SO:0001782  TF_binding_site_variant A sequence variant located within a transcription factor binding site.  SO:0001566  
SO:0001566  regulatory_region_variant   A sequence variant located within a regulatory region.  SO:0001878  SO:0001782

Answer 1

[jared.andrews07]

Just to be clear, a variant can lie in a coding region and still have regulatory impact. And "regulatory region" can mean different things depending on who you ask. Variants in enhancers may affect their activity as well as any transcripts (eRNAs, lncRNAs) that stem from them.

Regardless, if you're looking for variants in traditional enhancers/promoters, you'll likely want to focus on those marked with 1, 3, 4, 6, 7, 9, 14, 15, 32, and 33. That list doesn't include splice sites, which you could still make an argument for being 'regulatory', but I assume that variants leading to alternative isoforms isn't exactly what you want. I'm including 1 and 3, which are located in UTRs. I'm assuming some of these have multiple tags, and you'll likely want to focus on the obvious ones first (15, 32), though I don't know how these were annotated or what data sources are being used. The regulome is still being hashed out in many cell types/diseases, so those that aren't annotated with 15 or 32 may still well have regulatory impact.