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I am looking at genomic data (HG19). I have many SNPs, their chromosomes and positions. I want to look at certain SNP (suppose its chromosome is 1 and position 77,226,919), and extract all SNPs in distance 1mb from that SNP.

Are the HG19 position in terms of base-pairs? Meaning that I need to take all SNPs in position $77,226,919 \pm100,000$? Or is it something else?

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  • $\begingroup$ A megabase is 1_000_000; not 100_000. $\endgroup$ Nov 24, 2021 at 13:47

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Yes, they are base pair positions

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HG19 refers to the build used as the reference genome. To extend on what @Emily_Ensembl said, base pair positions may change between different builds.

Please look at the following link for a more detailed explanation: https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19

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