locateVariants returns genes from both Forward and Reverse strands in PRECEDEID and FOLLOWID

Inizia dalla documentazione e dall’implementazione di locateVariants() e IntergenicVariants(upstream=1000000, downstream=1000000), quindi esamina come vengono popolati PRECEDEID e FOLLOWID e come viene gestito il filamento. Il lavoro è completato quando l’interpretazione consapevole del filamento è documentata chiaramente, oppure quando il comportamento segnalato ha un test di regressione mirato e una correzione concordata.

Hello,

I'm looking at an intergenic variant (in the bovine genome) and want to figure the genes relative to which it is downstream or upstream, i.e. relative to the gene's position and its strand. I used locateVariants() with region=IntergenicVariants(upstream=1000000, downstream=1000000) in order to do this. However, some results puzzle me.

Here's what my variant looks like in the gene annotation results:

> all_var_df[rownames(all_var_df) == "AX-106756303", ]

             seqnames    start      end width strand   LOCATION LOCSTART LOCEND QUERYID TXID CDSID GENEID    PRECEDEID     FOLLOWID
AX-106756303        1 34617002 34617002     1      * intergenic       NA     NA       1 <NA>         <NA> ENSBTAG0.... ENSBTAG0....

Here's what PRECEDEID looks like:

lapply(all_var_df[rownames(all_var_df) == "AX-106756303", ]$PRECEDEID, function(X) {mapIds( org.Bt.eg.db, keys=X, column="SYMBOL", keytype="ENSEMBL", multiVals="first") } )

ENSBTAG00000019313 ENSBTAG00000016711 ENSBTAG00000003877 ENSBTAG00000044714 ENSBTAG00000020940 ENSBTAG00000020939 ENSBTAG00000001656 ENSBTAG00000045788 ENSBTAG00000006536 
           "ZMIZ1"             "PPIF"          "ZCCHC24"                 NA           "ANXA11"            "PLAC9"          "TMEM254"                 NA             "CL46" 

When looking closer at these genes in Ensembl, I notice that they are all located "to the right" of the SNP location on the forward strand and that some of them are on the Forward strand (e.g. ZMIZ1 and PPIF), while others are on the Reverse strand (e.g. ZCCHC24 and PLAC9):

https://oct2018.archive.ensembl.org/Bos_taurus/Location/View?db=core;g=ENSBTAG00000013264;r=28:34948822-35454825;t=ENSBTAT00000046662

This seems a bit confusing. Shouldn't the variant be considered upstream relative to the two genes on the Forward strand, and downstream relative to the genes in the Reverse strand?

How should the PRECEDEID gene list be interpreted, more precisely?