Venous return from the limbs is largely facilitated by the action of neighbouring skeletal muscles compressing the veins and forcing the blood proximally past the valves which prevent back flow. If you are inactive for a long time by sitting, or are sitting in such a way as to impede blood returning from your calves (i.e. with the back of your knees pressing into the edge of the chair) blood movement in this manner is greatly slowed.
Blood that is moving more slowly or turbulently has a greater propensity to coagulate and form a thrombus. This is similar to the rationale for prescribing anti coagulants to patients with atrial fibrillation - the turbulent and slow movement of blood through their atria leaves them at greater risk of throwing a clot to the brain causing a cerebrovascular accident.
Hypoxia isn't really that relevant in the case you describe as arterial supply is unaffected (much higher pressure) meaning tissues do not become ischaemic. There is also collateral venous drainage from the limb although this can subsequently cause problems in the form of post thrombotic syndrome. The most significant risk would be that of the thrombus breaking off and lodging in the lungs - a pulmonary embolism.