NA for several snps that overlap annotations

[meghatron21]

test.intersect.txt
Hi.

I have been using goshifter over the past weeks to better assess the overlap of some of my snps with epigenetic features I have downloaded from ENCODE.

I was primarily confused about SNPs that are showing up as "NA" in the .enrich files. When I do a simple bedtools intersect with SNPs that show up as "NA", there is overlap with features in the bed file that I downloaded. However, from my understanding, the NA is if a locus does not overlap any annotations. I don't know if I'm missing something, but I would love to understand what is going on.

Also, on another note, I have some X chromosome SNPs I'm interested in, but I noticed the link to LD files doesn't include chrX. I didn't know if there was an updated link

Thanks!
Meghana