Lets $X$ is a topological space and $Y$ is some subset of $X$. How we define topology of quotient space $$X/Y=\{x\in X~|~x\sim y\Leftrightarrow x, y\in Y\}.$$
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For a set $X$ and an equivalence relation $R$, the quotient set $X/R$ is the set of equivalence classes $[x]$ of $R$. The quotient set comes with a quotient map $\pi:X\rightarrow X/R$, naturally defined by sending $x$ to its equivalence class $[x]$. The "quotient topology" on $X/R$ is defined by saying "$U\subset X/R$ is open iff $\pi^{-1}(U)$ is open in $X$." (the quotient topology itself is a special case of two things: 1) the weak topology induced by a famaily of maps too/from your set, and 2) a pushout diagram. You should check these things out, they're cool.) Your example, quotienting by a subset, is a special case of a quotient set. To make your relation an equivalence relation, just add the diagonal $\Delta_X= \{ (x,x)\in X\times X\ |\ x\in X\}$. An element $[x]\in$"$X/Y$" is either a singleton $[x]=\{x\}$ (where $x\not\in Y$), or $[x]=Y$. Hence the quotient map is a bijection on $X-Y$. If $U\subset X/Y$, then $U$ is open iff $\pi^{-1}(U)=\{x\in X\ |\ [x]\in U\}$ is open in $X$. We can write any $U$ as $(U-\{Y\})\ \dot{\cup}\ (\{Y\}\cap U)$, so in general $U$ is open iff $\pi^{-1}(U)=\pi^{-1}(U-\{Y\})\ \dot{\cup}\ \pi^{-1}(\{Y\}\cap U)$ is open in X. Thus for $U\subset X/Y$: if $Y\not\in U$ then $\pi^{-1}(U)$ is disjoint from $Y\subset X$ so the quotient map is a bijection; if $Y\in U$, then we must check that $\{x\in X-Y\ |\ [x]\in U\}\cup Y$ is open in X. So if you want to think of $X/Y$ as "$X$, except $Y$ has collapsed" you can think "$U$ is open iff $U$ is open in $X$ and doesn't intersect $Y$, or $U\cup Y$ is open in $X$." |
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