In this context, the following could safely be inferred.
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What is is the number of participants in the marathon.
> "Every year, over 36,000 people, which is the largest scale in Japan, run/participate."
A literal translation would be close to impossible, which is why I used "the largest scale". A slightly more literal TL would be:
> "Every year, over 36,000 people, which is the most in Japan, run/participate (in this marathon)."