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I am looking at the PharmaPGKB database for SNPs and trying to understand what the following annotation means:

rs1801131 at 1:11854475 in CLCN6, MTHFR (VIP)

Ok, the SNP identified by rs1801131 occurs in the first chromosome, at position 11854475.

Then, the two genes' identifiers come. The position 11854475 is inside the gene MTHFR. Why do they also annotate the SNP to the gene CLCN6 (which is a "neighbour" of MTHFR) ?

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up vote 4 down vote accepted

It is because the two genes overlap:

enter image description here

CLCN6 is on the plus strand and MTHFR is on the minus strand. The SNP is annotated to both because it falls in a region of the genome claimed by both genes.

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