diff --git a/packages/core/ui/BaseTooltip.tsx b/packages/core/ui/BaseTooltip.tsx
index 3921ea289b..0465770659 100644
--- a/packages/core/ui/BaseTooltip.tsx
+++ b/packages/core/ui/BaseTooltip.tsx
@@ -1,4 +1,5 @@
 import {
+  offset,
   useClientPoint,
   useFloating,
   useInteractions,
@@ -43,6 +44,7 @@ export default function BaseTooltip({
   const { refs, floatingStyles, context } = useFloating({
     placement,
     strategy: 'fixed',
+    middleware: [offset(5)],
   })
 
   const clientPoint = useClientPoint(context, clientPointCoords)
diff --git a/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRenderer.ts b/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRenderer.ts
index cf56e37cd7..7cec141abb 100644
--- a/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRenderer.ts
+++ b/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRenderer.ts
@@ -15,17 +15,11 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
 
     const { makeImageData } = await import('./makeImageData')
 
-    const rest = await renderToAbstractCanvas(
-      width,
-      height,
-      renderProps,
-      async ctx => {
-        await makeImageData(ctx, {
-          ...renderProps,
-          features,
-        })
-        return undefined
-      },
+    const rest = await renderToAbstractCanvas(width, height, renderProps, ctx =>
+      makeImageData(ctx, {
+        ...renderProps,
+        features,
+      }),
     )
 
     const results = await super.render({
diff --git a/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRendering.tsx b/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRendering.tsx
index 8f96022b16..477061310b 100644
--- a/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRendering.tsx
+++ b/plugins/variants/src/MultiLinearVariantRenderer/MultiVariantRendering.tsx
@@ -1,14 +1,13 @@
-import { useRef } from 'react'
+import { useMemo, useRef } from 'react'
 
 import { PrerenderedCanvas } from '@jbrowse/core/ui'
 import { observer } from 'mobx-react'
+import RBush from 'rbush'
 
 import type { Source } from '../types'
 import type { Feature } from '@jbrowse/core/util'
 import type { Region } from '@jbrowse/core/util/types'
 
-// locals
-
 const MultiVariantRendering = observer(function (props: {
   regions: Region[]
   features: Map<string, Feature>
@@ -18,16 +17,51 @@ const MultiVariantRendering = observer(function (props: {
   sources: Source[]
   scrollTop: number
   totalHeight: number
+  rbush: RBush<{ genotype: string }>
+  displayModel: any
   onMouseLeave?: (event: React.MouseEvent) => void
   onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void
   onFeatureClick?: (event: React.MouseEvent, arg?: Feature) => void
 }) {
   const { totalHeight, scrollTop } = props
+  const { rbush, displayModel } = props
   const ref = useRef<HTMLDivElement>(null)
+  const rbush2 = useMemo(
+    () => new RBush<{ genotype: string }>().fromJSON(rbush),
+    [rbush],
+  )
+
+  function getFeatureUnderMouse(eventClientX: number, eventClientY: number) {
+    let offsetX = 0
+    let offsetY = 0
+    if (ref.current) {
+      const r = ref.current.getBoundingClientRect()
+      offsetX = eventClientX - r.left
+      offsetY = eventClientY - r.top
+    }
+    const ret = rbush2.search({
+      minX: offsetX,
+      maxX: offsetX + 3,
+      minY: offsetY,
+      maxY: offsetY + 3,
+    })
+    return ret[0]?.genotype
+  }
 
   return (
     <div
       ref={ref}
+      onMouseMove={e =>
+        displayModel.setHoveredGenotype?.(
+          getFeatureUnderMouse(e.clientX, e.clientY),
+        )
+      }
+      onMouseLeave={() => {
+        displayModel.setHoveredGenotype?.(undefined)
+      }}
+      onMouseOut={() => {
+        displayModel.setHoveredGenotype?.(undefined)
+      }}
       style={{
         overflow: 'visible',
         position: 'relative',
diff --git a/plugins/variants/src/MultiLinearVariantRenderer/makeImageData.ts b/plugins/variants/src/MultiLinearVariantRenderer/makeImageData.ts
index c5ba3508ce..fdc439a9f2 100644
--- a/plugins/variants/src/MultiLinearVariantRenderer/makeImageData.ts
+++ b/plugins/variants/src/MultiLinearVariantRenderer/makeImageData.ts
@@ -7,6 +7,7 @@ import {
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util'
 
 import type { MultiRenderArgsDeserialized } from './types'
+import RBush from 'rbush'
 
 const fudgeFactor = 0.6
 const f2 = fudgeFactor / 2
@@ -55,20 +56,27 @@ export async function makeImageData(
     features.values(),
     minorAlleleFrequencyFilter,
   )
+  const rbush = new RBush()
   for (const feature of mafs) {
     const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)
     const w = Math.max(Math.round(rightPx - leftPx), 2)
     const samp = feature.get('genotypes') as Record<string, string>
-    let t = -scrollTop
+    let y = -scrollTop
 
     const s = sources.length
     for (let j = 0; j < s; j++) {
       const { name, HP } = sources[j]!
       const genotype = samp[name]
       const x = Math.floor(leftPx)
-      const y = t
       const h = Math.max(rowHeight, 1)
       if (genotype) {
+        rbush.insert({
+          minX: x - f2,
+          maxX: x + w + f2,
+          minY: y - f2,
+          maxY: y + h + f2,
+          genotype,
+        })
         const isPhased = genotype.includes('|')
         if (renderingMode === 'phased') {
           if (isPhased) {
@@ -83,7 +91,10 @@ export async function makeImageData(
           drawColorAlleleCount(alleles, ctx, x, y, w, h)
         }
       }
-      t += rowHeight
+      y += rowHeight
     }
   }
+  return {
+    rbush: rbush.toJSON(),
+  }
 }