We construct a series of homomorphisms from the $Y$-filtration on the monoid of homology cylinders to torsion modules via the mod $\mathbb{Z}$ reduction of the LMO functor. The restriction of our homomorphism to the lower central series of the Torelli group does not factor through Morita's refinement of the Johnson homomorphism. We use it to show that the abelianization of the Johnson kernel of a closed surface has torsion elements. We also determine the third graded quotient $Y_3\mathcal{IC}_{g,1}/Y_4$ of the $Y$-filtration.