I would recommend Handbook of Korean Vocabulary by Miho Choo and William O'Grady (Amazon). It's not exactly a dictionary but it lists root words alphabetically and breaks down that root in words (native or Sino-Korean) with a rough English equivalent. It also gives the 한자 for Sino-Korean roots, if you're into that. For example, 생(生) - be born, life, student, etc. would list 생일 - birthday [~day] [~日].
I find it helps me if I learn a new (unfamiliar) vocab word to put it into context with words with similar roots which increases meaningful prediction of future vocab. You can do more or less that same thing with Naver but requires a little more effort.
Awesome book of many, many of these combos (both Hanja and pure Korean):
Handbook of Korean Vocabulary: A Resource for Word Recognition and Comprehension (English and Korean Edition) https://www.amazon.com/dp/0824818156/ref=cm_sw_r_cp_api_glt_fabc_V773JK05JVPVMHWZ2911
As technocracy90 said, for Hanja based words, you can just refer to the meaning of the individual Chinese characters. Check out any Hanja dictionary such as Naver's. Unfortunately, there are no online Hanja dictionaries designed for English speakers, so if you are a beginner, it may be frustrating.
For native Korean words, I have yet to find any good online resources for etymology. This book (Handbook of Korean Vocabulary) is the only detailed source I have seen so far. It covers both Hanja and native Korean words.
https://www.amazon.com/Handbook-Korean-Vocabulary-Recognition-Comprehension/dp/0824818156/
If you're interested in this kind of thing more generally, I found this cool book at my local library: https://www.amazon.com/Handbook-Korean-Vocabulary-Recognition-Comprehension/dp/0824818156/ref=sr_1_2?ie=UTF8&qid=1521745556&sr=8-2&keywords=handbook+of+korean+vocabulary
in which you can look up words or morphemes and it tells you their derivation and what other words they are in.
Over 60% of Korean vocabulary descended from Chinese. So that should really help you with words. Some Chinese (Sino-Korean is the term used) roots are the basis of dozens of Korean nouns, and nouns are turned into verbs, adverbs, modifiers, etc. in a very systematic way. Many dictionaries show the Chinese character when the root is based on it and I suggest buying this book to get you going: http://www.amazon.com/Handbook-Korean-Vocabulary-Recognition-Comprehension/dp/0824818156/
I agree with this. I've got the Handbook of Korean Vocabulary and am in the process of making an anki deck out of it (search for Sino-Korean roots; sorry for how slow my progress has been). I'm also in the process of learning Mandarin (after I'd already made some progress with Korean), so it makes a little more sense for me to study Korean this way. Even if you're not interested in learning Chinese, I think it's still smart to pay attention to hanja when it comes up and always try to make connections between words.
> Where did you get the vocabulary from? Is there a free data source?
Not OP, but the idea behind the website is also used in Handbook of Korean Vocabulary: A Resource for Word Recognition and Comprehension. The book lists vocabulary by hanja, so you'd have all the vocab using 家 가 together, then the vocab using 歌 가, etc. It's a nice idea - both the book and website - as instead of 'just words' you can use it to memorize related concepts.
For a free data source, why not Naver's Hanja Dictionary site? For example, looking up 地 지 gives quite a few results using that hanja.
Many Koreans as they go through their education take tests regarding their knowledge of Hanja. There are several companies that offer them. You can learn more here. And if you go to this website it tells you what characters are needed to know for each level. 8 is the lowest level and 특급 is the highest. For each test you need to know all of the previous levels' hanja as well. This is also a great book. Here is a page of what the inside looks like. I hope this points you in the right direction.