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Where Can I Get Gene Name Annotations By Position

For a university project I need a file containing the gene names and their positions on the hg19 chromosome 1. For this reason I downloaded a .bed file from USCS containing entries such as

chr1    248457917   248458880   uc010pzj.2  0   -   248457917   248458880   0   1   963,    0
chr1    248436153   248437116   uc010pzi.2  0   -   248436153   248437116   0   1   963,    0,

However I believe these are USCS identifiers (they can map to gene names) and not gene names. How can I map these identifiers to gene names, or where can I download data containing gene names and their locations? I know very little about genetics, I have searched the USCS downloads page but I was not able to find anything.

Thank you in advance.

hg19 uscs

1 answer

$ wget -qO - "http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/kgXref.txt.gz" | gunzip -c | grep -wE '(uc010pzj\.2|uc010pzi\.2)'

uc010pzi.2  NM_001004695    Q8NG76  O2T33_HUMAN OR2T33  NM_001004695    NP_001004695    Homo sapiens olfactory receptor, family 2, subfamily T, member 33 (OR2T33), mRNA.       
uc010pzj.2  NM_001004692    Q8NG77  O2T12_HUMAN OR2T12  NM_001004692    NP_001004692    Homo sapiens olfactory receptor, family 2, subfamily T, member 12 (OR2T12), mRNA.       

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