diff --git a/js/roi/ROIManager.js b/js/roi/ROIManager.js
index 0a4a4757a..86fc49f40 100644
--- a/js/roi/ROIManager.js
+++ b/js/roi/ROIManager.js
@@ -274,6 +274,10 @@ class ROIManager {
         return this.roiSets.find(roiSet => true === roiSet.isUserDefined)
     }
 
+    deleteUserDefinedROISet(){
+        this.roiSets = this.roiSets.filter(roiSet => roiSet.isUserDefined !== true);
+    }
+    
     initializeUserDefinedROISet() {
 
         const config =
@@ -289,15 +293,8 @@ class ROIManager {
     }
 
     async deleteRegionWithKey(regionKey, columnContainer) {
-
         columnContainer.querySelectorAll(createSelector(regionKey)).forEach(node => node.remove())
 
-        const {feature, set} = await this.findRegionWithKey(regionKey)
-
-        if (set) {
-            set.removeFeature(feature)
-        }
-
         const records = await this.getTableRecords()
 
         if (0 === records.length) {
@@ -307,23 +304,6 @@ class ROIManager {
 
     }
 
-    async findRegionWithKey(regionKey) {
-
-        const {chr, start, end} = parseRegionKey(regionKey)
-
-        for (let set of this.roiSets) {
-            const features = await set.getFeatures(chr, start, end)
-
-            for (let feature of features) {
-                if (feature.chr === chr && feature.start >= start && feature.end <= end) {
-                    return {feature, set}
-                }
-            }
-        }
-
-        return {feature: undefined, set: undefined}
-    }
-
     toJSON() {
         return this.roiSets.map(roiSet => roiSet.toJSON())
     }
diff --git a/js/roi/ROIMenu.js b/js/roi/ROIMenu.js
index e037215f7..c13cbfea9 100644
--- a/js/roi/ROIMenu.js
+++ b/js/roi/ROIMenu.js
@@ -109,9 +109,16 @@ class ROIMenu {
                 '<hr/>',
                 {
                     label: 'Delete',
-                    click: () => {
-                        this.browser.roiManager.deleteRegionWithKey(regionElement.dataset.region, this.browser.columnContainer)
-                        this.browser.roiManager.repaintTable()
+                    click: async () => {
+                        roiSet.removeFeature(feature)
+                        const userDefinedFeatures = await roiSet.getAllFeatures()
+                        
+                        // Delete user defined ROI Set if it is empty
+                        if (Object.keys(userDefinedFeatures).length === 0) {
+                            roiManager.deleteUserDefinedROISet()
+                        }
+                        roiManager.deleteRegionWithKey(regionElement.dataset.region, columnContainer)
+                        roiManager.repaintTable()
                     }
                 }
             )
diff --git a/js/roi/ROISet.js b/js/roi/ROISet.js
index e97bbd845..2880f5de5 100644
--- a/js/roi/ROISet.js
+++ b/js/roi/ROISet.js
@@ -184,6 +184,10 @@ class DynamicFeatureSource {
         if (this.featureMap[chr]) {
             const match = `${chr}-${start}-${end}`
             this.featureMap[chr] = this.featureMap[chr].filter(feature => match !== `${feature.chr}-${feature.start}-${feature.end}`)
+            // Check if featureMap for a specific chromosome is empty now and delete it if yes
+            if (this.featureMap[chr].length === 0) {
+                delete this.featureMap[chr];
+            }
         }
     }
 }