In this paper, we study the class of polytopes which can be obtained by taking the convex hull of some subset of the points
$\{e_i-e_j \ \vert \ i \neq j\} \cup \{\pm e_i\}$ in
$\mathbb {R}^n$, where
$e_1,\dots ,e_n$ is the standard basis of
$\mathbb {R}^n$. Such a polytope can be encoded by a quiver Q with vertices
$V \subseteq \{{\upsilon }_1,\dots ,{\upsilon }_n\} \cup \{\star \}$, where each edge
${\upsilon }_j\to {\upsilon }_i$ or
$\star \to {\upsilon }_i$ or
${\upsilon }_i\to \star $ gives rise to the point
$e_i-e_j$ or
$e_i$ or
$-e_i$, respectively; we denote the corresponding polytope as
$\operatorname {Root}(Q)$. These polytopes have been studied extensively under names such as edge polytope and root polytope. We show that if the quiver Q is strongly-connected, then the root polytope
$\operatorname {Root}(Q)$ is reflexive and terminal; we moreover give a combinatorial description of the facets of
$\operatorname {Root}(Q)$. We also show that if Q is planar, then
$\operatorname {Root}(Q)$ is (integrally equivalent to) the polar dual of the flow polytope of the planar dual quiver
$Q^{\vee }$. Finally, we consider the case that Q comes from the Hasse diagram of a finite ranked poset P and show in this case that
$\operatorname {Root}(Q)$ is polar dual to (a translation of) a marked order polytope. We then go on to study the toric variety
$Y(\mathcal {F}_Q)$ associated to the face fan
$\mathcal {F}_Q$ of
$\operatorname {Root}(Q)$. If Q comes from a ranked poset P, we give a combinatorial description of the Picard group of
$Y(\mathcal {F}_Q)$, in terms of a new canonical ranked extension of P, and we show that
$Y(\mathcal {F}_Q)$ is a small partial desingularisation of the Hibi projective toric variety
$Y_{\mathcal {O}(P)}$ of the order polytope
$\mathcal {O}(P)$. We show that
$Y(\mathcal {F}_Q)$ has a small crepant toric resolution of singularities
$Y(\widehat {\mathcal {F}}_Q)$ and, as a consequence that the Hibi toric variety
$Y_{\mathcal {O}(P)}$ has a small resolution of singularities for any ranked poset P. These results have applications to mirror symmetry [61].