In my current AWS account, I have only one instance in Us-West -2. I do not have a ELB. The Elastic IP is in the same region. It does not specify any availability zone. but wrt RDS, this instance is connected to in a different availability zone of the same region and it also access few S3 buckets created in other region.. Is it why I am getting charged? any thoughts on this will be appreciated.
Any inter-AZ traffic like EC2 in AZ-A to RDS in AZ-B will incur inter-AZ traffic charges. I suggest you move your resources into one AZ to eliminate those charges. One fairly easy way to do this is to snapshot the EC2 / RDS and create a new one based on the image. If you need instructions search for "Move AWS EC2 instance to another availability zone" or similar.
S3 access isn't inter-AZ, it's either via the internet gateway or the VPC endpoint. Make sure you provision an S3 gateway endpoint (not interface endpoint) in your VPC that way S3 traffic is free.