Etymology
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supra- 
word-forming element meaning "above, over, beyond, before," from Latin supra "above, over, before, beyond, on the upper side," in supera (parte), literally "on the upper (side)," from old fem. ablative singular of superus (adj.) "above," related to super "above, over" (from PIE root *uper "over"). In English interchangeable with, but somewhat more technical than, super-. Rare as a prefix in Latin, more common in Medieval Latin, in English chiefly scientific or technical.
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hyper- 
word-forming element meaning "over, above, beyond," and often implying "exceedingly, to excess," from Greek hyper (prep. and adv.) "over, beyond, overmuch, above measure," from PIE root *uper "over."
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sur- (1)
word-forming element meaning "over, above, beyond, in addition," especially in words from Anglo-French and Old French, from Old French sour-, sor-, sur-, from Latin super "above, over," from PIE root *uper "over."
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super- 
word-forming element meaning "above, over, beyond," from Latin super (adverb and preposition) "above, over, on the top (of), beyond, besides, in addition to," from *(s)uper-, variant form of PIE root *uper "over." In English words from Old French, it appears as sur-. The primary sense seems to have shifted over time from usually meaning "beyond" to usually meaning "very much," which can be contradictory. E.g. supersexual, which is attested from 1895 as "transcending sexuality," from 1968 as "very sexual."
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hypso- 
word-forming element meaning "height," from Greek hypsos "height, top," from PIE *upso-, from root *upo "under," also "up from under," hence also "over" The Greek word is cognate with Sanskrit os "above, over," Old Church Slavonic vysoku "high."
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preter- 

also praeter-, word-forming element meaning "beyond; over, more than in quantity or degree," from Latin praeter (adverb and preposition) "beyond, before, above, more than," properly comparative of prae "before," from PIE root *per- (1) "forward," hence "in front of, before."

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ana- 

before vowels an-, word-forming element meaning: 1. "upward, up in place or time," 2. "back, backward, against," 3. "again, anew," from Greek ana (prep.) "up, on, upon; up to, toward; throughout; back, backwards; again, anew," from an extended form of PIE root *an- (1) "on, upon, above" (see on, which is the English cognate). In old medical prescriptions, ana by itself meant "an equal quantity of each."

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over- 

word-forming element meaning variously "above; highest; across; higher in power or authority; too much; above normal; outer; beyond in time, too long," from Old English ofer (from PIE root *uper "over"). Over and its Germanic relations were widely used as prefixes, and sometimes could be used with negative force. This is rare in Modern English, but compare Gothic ufarmunnon "to forget," ufar-swaran "to swear falsely;" Old English ofercræft "fraud."

In some of its uses, moreover, over is a movable element, which can be prefixed at will to almost any verb or adjective of suitable sense, as freely as an adjective can be placed before a substantive or an adverb before an adjective. [OED]

Among the old words not now existing are Old English oferlufu (Middle English oferlufe), literally "over-love," hence "excessive or immoderate love." Over- in Middle English also could carry a sense of "too little, below normal," as in over-lyght "of too little weight" (c. 1400), overlitel "too small" (mid-14c.), overshort, etc.

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epi- 

before vowels reduced to ep-, before aspirated vowels eph-, word-forming element meaning "on, upon, above," also "in addition to; toward, among," from Greek epi "upon, at, close upon (in space or time), on the occasion of, in addition," also "after," from PIE *epi, *opi "near, at, against" (source also of Sanskrit api "also, besides;" Avestan aipi "also, to, toward;" Armenian ev "also, and;" Latin ob "toward, against, in the way of;" Oscan op, Greek opi- "behind;" Hittite appizzis "younger;" Lithuanian ap- "about, near;" Old Church Slavonic ob "on"). A productive prefix in Greek; also used in modern scientific compounds (such as epicenter).

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a- (1)

prefix or inseparable particle, a relic of various Germanic and Latin elements.

In words derived from Old English, it commonly represents Old English an "on, in, into" (see on (prep.)), as in alive, above, asleep, aback, abroad, afoot, ashore, ahead, abed, aside, obsolete arank "in rank and file," etc., forming adjectives and adverbs from nouns, with the notion "in, at; engaged in." In this use it is identical to a (2).

It also can represent Middle English of (prep.) "off, from," as in anew, afresh, akin, abreast. Or it can be a reduced form of the Old English past participle prefix ge-, as in aware.

Or it can be the Old English intensive a-, originally ar- (cognate with German er- and probably implying originally "motion away from"), as in abide, arise, awake, ashamed, marking a verb as momentary, a single event. Such words sometimes were refashioned in early modern English as though the prefix were Latin (accursed, allay, affright are examples).

In words from Romanic languages, often it represents reduced forms of Latin ad "to, toward; for" (see ad-), or ab "from, away, off" (see ab-); both of which by about 7c. had been reduced to a in the ancestor of Old French. In a few cases it represents Latin ex.

[I]t naturally happened that all these a- prefixes were at length confusedly lumped together in idea, and the resultant a- looked upon as vaguely intensive, rhetorical, euphonic, or even archaic, and wholly otiose. [OED]
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