Common banks across online shoping websites for purchasing product?

I am sorry to let you know that for online purchases, the e-commerce sites do not accept "Savings Bank Accounts" for their EMI schemes.
To go for EMI schemes you have to have a Credit Card of any of the banks. Even then the interest rates do not depend on the banks, but it is on the products and the site from where you are purchasing. Different products, their price range and the tenure you choose to pay, rather say you get to choose are the deciding factors of the interest rates.
You get to know the interest rates for a particular product from the page of the product itself, where you need to click on the "EMI options". A separate page or a list will appear where you will get to know the interest rates per tenure.
But as as said as above you need to have a credit card for availing the EMI option.

EMI schemes are limited to the credit cards. So you opening account in any bank would not make much difference if you choose to not have a credit card. However if you wish to have a credit card in near future and deciding to have savings bank account for the same can avail you for the EMI schemes on those site. In such case it'd be good for you to choose one of the banks from the below list for credit card as they have a lot of support across e-commerce websites for EMI scheme. HDFC bank, AXIS bank, ICICI bank, SBI Bank, Standard charted, Kotak bank. These are the banks that flipkart and Amazon have association with for the EMI scheme.

Please let me know which bank account holds low interest for ex. in Flipkart Kotak and Axis bank holds low(12%) interest on product.

That's subjective and there is no fixed answer.The interest rate will vary for those banks depending on the product in same site. Also do note that some banks have the zero interest schemes which usually charge higher for product but allow EMI plans in them.

So finally comment the most common banks(holding low interest) available in sites like amazon.com for payment in EMI.

If you are completely unsure of which bank to choose for credit card and for the amazon.com payments in EMI scheme, then best option is to check the EMI offers on official page. You can see the EMI scheme from banks on the product page. Clicking on link will show the banks allowing the EMI for that product. Try to find out common banks across various products in EMI offer and then choose the bank for your saving bank and credit card.

Well, if you would wish to open a savings bank account only with an aim to get a debit card that can be used on the E Commerce sites with a view to get access to EMI payment options, then I would have to disappoint you. None of the E Commerce sites allow EMI facility on debit cards or net banking transactions. If you want to get the EMI facility, you will need to opt for credit cards.

If you decide to get a credit card, you can do so by having a fixed deposit in the bank of your choice. Almost all banks offer credit card for an amount equivalent to 80 percent of your Fixed deposit. The major E Commerce sites like Amazon and Flipkart provide EMI facility for the credit cards from the following banks -

HDFC
Citi
ICICI
Kotak
Axis
IndusInd
SBI
Standard Chartered
HSBC

The rate of interest varies from product to product and bank to bank on the same site. The EMI options are available for different tenures like 3,6,9,12,18 and 24 months.

As for your query of which banks charge lower rate of interest, I do not think there is a fixed answer for this. The rate of interest charged is normally 12 percent for most of the banks. The rate differs depending upon the transaction amount and the tenure. It may also differ from product to product.

The best strategy would be to choose the product across multiple sites and choose the one that meets your expectations.