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According to the most authentic Sunni and Shia books of Hadeeth and Tafseer of the Holy Qur'an, there are numerous verses in the Holy Qur'an which have implied references to Ameerul Mo’mineen Ali (AS). According to the well known companion Ibn  Abbas there are as many as 300 verses in the Holy Qur'an which truer to the tributes of Ameerul Mo;mineen Ali (AS). This has been mentioned in many Sunni books like Tareekh Dimishq by Ibn Asaakir and Al-Sawaa’iq by Inb Hajar Al-Haythami , page 186 and  al-Soyooti  in Tareekh Al-Khulafaa , page 171 , and by Al-Khateeb Al-Baghdadi in Tareekh Baghdad, V. 6 P.221. 
Ibn Hanbal , the founder of Hanbali sect said : No one from the companions was praised in authentic Hadeeths more than Ali Ibn Abi Talib. (Al-Haakim Al-Nisaburi in Al-Mustadrak V,3, P.107).
According to the most authentic Sunni books, these are some of the verses which refer to HIman Ali (AS):
1. Sura 3 Verse 61
"And whoso disputeth with thee concerning him, after the knowledge which hath come unto thee, say (unto him): Come! We will summon our sons and your sons, and our women and your women, and ourselves and yourselves, then we will pray humbly (to our Lord) and (solemnly) invoke the curse of Allah upon those who lie."
This verse alludes the deputation of the Nazareth of Najran who came to Medina to hold a discussion with the holy Prophet about the truth of Islam. In this verse, the reference to "our sons, and our women" includes references to Ali, Fatima, Hasan and Hussain.
2. Sura 5,Verse 55
"Your Master is only Allah and His Messenger, and the believers who observed prayer and pay the poor rate during Rukoo’."
According to the Traditions, "the believers" referred to in this verse includes a reference to  Imam Ali (AS).
3. Sura 7,Verse 181
"And of those We have created, there are people that guide men in the truth, and do justice therewith."
According to the Traditions, the reference to "people that guide men with truth" includes a reference to  Imam Ali (AS).
4. Sura 8,Verse 64
"O Prophet! Allah is sufficient for you and for such of the followers as follow you."
5. Sura 9 Verse 3
"And a proclamation from Allah and His messenger to all men on the day of the Greater Pilgrimage that Allah is free from obligation to the idolaters, and (so is) His messenger. So, if ye repent, it will be better for you; but if ye are averse, then know that ye cannot escape Allah. Give tidings (O Muhammad) of a painful doom to those who disbelieve."
In pursuance of this verse, the holy Prophet commissioned Hazrat Ali to go to the 'Greater Pilgrimage' to announce the verses of the Sura "Immunity" wherein God absolved the Muslims from all obligations under treaties previously concluded with the idolaters.
6. Sura 11 Verse 17
"Is he to be counted equal with those who rely on a clear proof from his Lord and the witness from Him recites it, and before it was the Book of Moses, and example and a mercy? Such believe therein. Whoso disbelieves therein, the Fire is his appointed place. So be not you in doubt concerning it. Lo, it is the truth from your Lord, but most of mankind believe it not."
One day, in one of his sermons, Imam Ali said that there was hardly a man from among to the Quraish who had not been referred to in the Holy Qur'an. Imam Ali was asked to recite some verse which alluded to him. Thereupon he recited the above verse.
7. Sura 13,Verse 43
"And those who disbelieve say 'you are not a Messenger' say to them, 'sufficient is Allah as the witness between me and you, and so is he who possesses knowledge of the Book."
According to commentators, the phrase "whosoever has the knowledge of the Book" alludes to Imam Ali (As).
8. Sura 24, Verse 36
"The lamp of light is lit in houses which Allah has allowed to be exalted so that His name be remembered in them. Therein He is glorified in the mornings and evenings."
According to the Traditions, the holy Prophet said that be "houses" referred to in this verse include the house of Ali and Fatima.
9. Sura 25,Verse 54
"And He it is Who created man from water, and has appointed for him kindred by blood, and kindred by marriage, and your Lord is all powerful."
According to the Traditions, "kindred by blood and kindred by marriage" refers to Imam Ali.
10. Sura 32,Verse 18
"Is he who is a believer like him who is an evil doer? Verily they are not equal." According to Ibn Abbas, "believer" in this verse refers to Imam Ali, and "evil doer"
refers to Walid b. Utba.
11. Sura 33, Verse 33
"And He it is Who created man from water, and has appointed for him kindred by blood, and kindred by marriage, and your Lord is all powerful."
Hazrat Ali is obviously included in the expression "Folk of the Household."
12. Sura 42,Verse 23
"Say O Muhammad to mankind: 'No reward do I ask of you for this except the love of my Progeny)
According to Traditions, when the holy Prophet was asked as to who were the relatives alluded to in the verse, the holy Prophet said, "Verily, the reference is to Ali, Fatima, Hasan and Hussain."
13. Sura 43,Verse 57
"And when the son of Mary is cited as an example, lo, the people jeer thereat."
According to the Traditions, the holy Prophet is said to have told Hazrat Ali that one day his example would be like that of Jesus Christ. A section of the people would love him so much that they would willingly die for him, whereas there would also be other people who would fight against him.
14. Sura 45,Verse 21
"Do those who commit evil deeds suppose that We shall treat them like those who believe and do good deeds - that their lives and their deaths shall be equal.No, bad is their judgment."
According to Ibn Abbas, "the doers of good" cited to in this verse, refer to to to Imam Ali, Hamza and Ubaydah b. Harith.
15. Sura 48,Verse 29
"Muhammad is the Apostle off God. And those with Him are firm against the disbelievers, and Merciful amongst themselves. Thus see them bowing down, and prostrating themselves in prayer, seeking grace from Allah and His pleasure. Their mark is upon their faces, being the traces of prostrations. Such is their description in the Torah. And their description in the gospel is like a seed that sends forth its sprout, then makes its strong; it then becomes thick, and stands on its stem, delighting the sowers, and causing the disbelievers to burn with rage at the sight of them. Allah has promised to those of them who believe and do good works, forgiveness and a great We reward."
According to the commentary of Imam Abu Musa, this verse was revealed in favour of Imam Ali
16. Sura 58 Verse 12
"O ye who believe! When you consult the Messenger in private, give alms before your consultation. That is better and purer for you. But when you do not find the wherewithal, Lo! Allah is Forgiving and Merciful."
According to the Traditions, when this verse was revealed the holy Prophet wanted to fix an amount which every person who consulted the holy Prophet should pay. Imam Ali contended that since the people were generally poor no amount should be fixed and the option should rest with the person concerned, to pay whatever alms he could.
17. Sura 66, Verse 4
"Now if both of you turn to Allah repentant, it will be better for you as your hearts are already so inclined. But if you backup each other against him, surely Allah is his helper, and Gabriel and the righteous among the believers, and furthermore, all other angels too are his helpers."
According to Ibn Abbas, the holy Prophet said that the "righteous men" alluded to as "helper" in this verse, refers to Ali (AS).
These are just few verses among many other verses praising Imam Ali (AS).
It is worth mentioning that there are books compiled by prominent scholars on the Quranic verses praising Ameerul Mo’mineen ali (As).
Wassalam.