Your code has a few problems which I’ll try to point out:
count = 0
prime = []          # this is obviously meant to collect all primes
candidate = []      # what is this supposed to do then though?
x = 2
y = 1               # never used
while count < 1000: # you start at `count = 0` but never increase the count
                    # later on, so would loop forever
    x = x+1
    if x > 1: # x is always bigger than 1 because you started at 2
              # and only increase it; also, you skipped 2 itself
        if x%2 != 0:                      # here, all you do is check if the
            if x%3 != 0:                  # number is dividable by any prime you
                if x%5 != 0:              # know of
                    if x%7 != 0:          # you can easily make this check work
                        if x%11 != 0:     # for any set (or list) of primes
                            if x%13 != 0: #
                                candidate.append(x) # why a candidate? If it’s
                                                    # not dividable by all primes
                                                    # it’s a prime itself
So, building on this, you can make it all work:
primes = [2] # we're going to start with 2 directly
count = 1    # and we have already one; `2`
x = 2
while count < 1000:
    x += 1
    isPrime = True          # assume it’s a prime
    for p in primes:        # check for every prime
        if x % p == 0:      # if it’s a divisor of the number
            isPrime = False # then x is definitely not a prime
            break           # so we can stop this loop directly
    if isPrime:             # if it’s still a prime after looping
        primes.append(x)    # then it’s a prime too, so store it
        count += 1          # and don’t forget to increase the count
Where did the p in the for loop come from?
for x in something is a construct that will loop over every element in something and for each iteration it gives you a variable x that will contain the current value. So for example the following will separately print 1, 2, 3.
for i in [1, 2, 3]:
    print(i)
Or for a list of primes, for p in primes will loop over all your stored primes and in each iteration p will be one prime from the list.
So the whole check will essentially loop over every known prime, and for each prime it will check if said prime is a divisor of the number. And if we find one prime for which this is the case, we can abort the loop, because the current number is definitely not a prime itself.