Etymology
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Words related to yes

yea (adv.)
Old English gea (West Saxon), ge (Anglian) "so, yes," from Proto-Germanic *ja-, *jai-, a word of affirmation (source also of German, Danish, Norwegian, Swedish ja), from PIE *yam-, from pronominal stem *i- (see yon). As a noun, "affirmation, affirmative vote," from early 13c.
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*es- 

Proto-Indo-European root meaning "to be."

It forms all or part of: absence; absent; am; Bodhisattva; entity; essence; essential; essive; eu-; eucalyptus; Eucharist; Euclidean; Eudora; Eugene; eugenics; eulogy; Eunice; euphemism; euphoria; euthanasia; homoiousian; improve; interest; is; onto-; Parousia; present (adj.) "existing at the time;" present (n.2) "what is offered or given as a gift;" proud; quintessence; represent; satyagraha; sin; sooth; soothe; suttee; swastika; yes.

It is the hypothetical source of/evidence for its existence is provided by: Sanskrit asmi, Hittite eimi, Greek esti-, Latin est, Old Church Slavonic jesmi, Lithuanian esmi, Gothic imi, Old English eom, German ist.

Y 
a late-developing letter in English. Called ipsilon in German, upsilon in Greek, the English name is of obscure origin. The sound at the beginning of yard, yes, yield, etc. is from Old English words with initial g- as in got and y- as in yet, which were considered the same sound and often transcribed as Ȝ, known as yogh. The system was altered by French scribes, who brought over the continental use of -g- and from the early 1200s used -y- and sometimes -gh- to replace Ȝ. As short for YMCA, etc., by 1915.
yeah 
American English, colloquial, by 1863, from drawling pronunciation of yes.
yep 

by 1889, American English, variant of yes or yeah, altered for emphasis, or possibly influenced by nope.

yup 
1906, variant of yes.