Transport Scotland has told people to avoid travelling on the roads and Network Rail has shut down all train services.
The rest of the UK is braced as the storm, with 100mph winds, is expected to move south.
Communities on England’s east coast are being told to prepare later for the most serious tidal surge for 30 years.
The Environment Agency expects 3,000 properties to be flooded within the next 24 hours.
A lorry driver has died after his HGV was blown on top of two cars in West Lothian.
Police in Scotland warned motorists of ongoing incidents due to fallen trees, flash flooding, overturned HGVs and minor road crashes.
BBC weather presenter Matt Taylor explained that “storm surges” are expected later.
He said surges begin when a rising area of low pressure takes pressure off the surface of the sea, allowing it “bulge” upwards.
“Then, as that pulls away, you get the very strong winds on the back edge of the low pressure and then that shoves that bulge of high sea levels down through the North Sea,” he said.
The Environment Agency said the North Sea coast from Northumberland to the Thames Estuary was at risk.
In some places sea levels could be as high as those during the devastating floods of 1953 – although flood defences built since then meant many parts of the country were now better protected, it added.
The agency has more than 100 flood warnings and alerts in place, including 18 severe alerts for the East Anglia region – indicating danger to life.
Those likely to be affected include West Mersea in Essex, Southwold and Thorpeness in Suffolk, the Riverside Business park in Lowestoft, Suffolk, and along the Bure and Yare rivers in Great Yarmouth.
Environment Agency flood risk manager Pete Fox told BBC Breakfast that people in these coastal areas need to think about taking action to prepare themselves now.
He said: “The most important thing actually is that along the East Coast, the high tide will be hitting in the hours of darkness this evening and tonight so people really need to take the daylight hours today to prepare for the coastal and tidal flooding that we’re predicting.
“We’ve been working with the emergency services for the last 24 hours or so gearing up for this event.”
Police in Norfolk, Suffolk and Essex are on alert to help the Environment Agency in an emergency period expected to last about 36 hours.
Norfolk’s deputy Chief Constable Charlie Hall said: “A multi-agency co-ordinating group has been convened twice to ensure appropriate plans and resources are in place.
“The group is planning for potential disruption for a prolonged period of up to 36 hours and households in those affected areas should be mindful of this.”
Other areas and services affected include:
- Network Rail has cancelled all trains in Scotland and is warning travellers to expect delays in northern and eastern England.
- Virgin Trains says no trains will run north of Carlisle until further notice and onward travel by any means cannot be guaranteed.
- East Coast says it will run a revised timetable.
- 100,000 homes in Scotland are now without power due to disruption caused by the storm.
- Northern Ireland Electricity says there are 6,500 customers without power.
- Glasgow, Edinburgh and Aberdeen airports have all cancelled a number of flights.
- Passengers at Leeds Bradford airport have been warned to expect delays.
- The Thames Barrier is due to close on Thursday night to protect London from floods.
In Scotland, the Scottish Environment Protection Agency has issued 11 flood warnings for Central; Edinburgh and Lothians; Fife; and Skye and Lochaber.
The Met Office has recorded gusts of 106mph at Glenogle in Stirlingshire and 114mph on the slopes of Aonach Mor near Fort William.
Regions under the Met Office’s amber “be prepared” warning are Central, Tayside and Fife; East Midlands; East of England; Grampian; Highlands and Eilean Siar; North East England; North West England; Orkney and Shetland; South West Scotland, Lothian and Borders; Strathclyde; and Yorkshire and Humber.
This warning indicates likely travel delays from road and rail closures, power cuts and damage to properties.
London and South East England; Northern Ireland; Wales; and West Midlands have been placed under a yellow warning.
This tells people in the area to be aware of the possibility of severe weather and to expect some disruption to their activities and travel plans.
Forecasters say snow is likely to fall in the north of Scotland on Thursday, up to 5cm deep on low ground with 20cm possible on higher ground.
Conditions across the UK are expected to have improved by the weekend.