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Time until a customer comes to a store since the last customer is a waiting time. Suppose there are 10 customers in a day, we can collect 10 waiting times (e.g., 48 min, 3 min, etc.). Based on the 10 values, we can compute a variance. I don't know if when talking about variance or variation in a quantity, the quantity should be in singular or plural.

The variance in waiting time was higher for Store A than Store B.
The variance in waiting times was higher for Store A than Store B.
The variance of waiting time was higher for Store A than Store B.
The variance of waiting times was higher for Store A than Store B.
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I'm a statistician. "Variance of waiting time" is how I would word this and how I have seen it worded elsewhere. This is similar to other uses of variance. We say the "variance of weight" or "variance of income" etc.

So, "of" and singular.

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You can use either:

The variable you are measuring is "the waiting time". The set of data you generated would be the set "of (the) waiting times". A pure mathematician would likely use the former (as posted above), a computer programmer implementing the algorithm for variance would likely use the latter. But both would understand each other.

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