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describe('Enter Base API URL', function() {   
  it('1st scenario', function() {  
  // Take any URL.   
  browser.get('xyz.com');   
  browser.ignoreSynchronization=true;  
  var user= by.xpath('//input[@name="username"]');  
  });

  it("2nd scenario", function() {   
  browser.driver.findElement(user).sendKeys('hi');   
  });   
browser.close();
});

How can I use this user variable in my second it block?

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Ideally, this user field should be defined in a separate "page object".

As far as two tests under describe go, it is just about defining a variable in a "higher" scope:

describe('Enter Base API URL', function() {   
    var user;

    it('1st scenario', function() {  
        // Take any URL.   
        browser.get('xyz.com');   

        browser.ignoreSynchronization=true;  
        user = by.xpath('//input[@name="username"]');  
    });

    it("2nd scenario", function() {   
        browser.driver.findElement(user).sendKeys('hi');   
    });   
});

Note that user = by.xpath('//input[@name="username"]'); by itself would do nothing, protractor/selenium would not try to locate the element at this point. Only when you are actually using the element, it would locate it on a page.

Also, note that protractor introduces the concepts of an ElementFinder - meaning, you should probably be using element() as opposed to browser.driver.findElement().

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