What is on each side of flapper?

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Carolina Blue

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My upstairs toilet runs occasionally when I flush my downstairs toilets. I opened its top and noticed on each side of the flapper is some sort of buildup (see picture). Neither of my toilets downstairs has this. Any idea what this is. Thank you for your help. Toilet.jpg
 
I can't tell for sure, but it looks to me like someone used plumbers putty over top of the tank to toilet bolts. Perhaps there was a slight leak at one time?

If so, you can remove the putty, and buy new tank to toilet brass bolts, which will come with rubber washers.
 
As far as "upstairs toilet runs occasionally when I flush my downstairs toilets", I would suggest that while you have that cover off, have someone flush the downstairs toilet and observe exactly what's happening. Is it just adding a little more water to the tank? Or is it letting a little water enter the bowl, which in turn is causing the water to refill tank slightly?

As far as those globs over the bolt heads, I would leave well enough alone unless you have a leak between the tank and the bowl.
 

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