Hello, a simple google search ("gencode lncrna database") can give you the partial answer: you can find lncRNA annotations here: http://www.gencodegenes.org/releases/current.html. Then, you'll have to map your SNPs to the lncRNA genes probably by analyzing some kind of genomic sequencing (using GATK for example) to find the genomic locations of your SNPs. You can also exploit SNP databases, such as dbSNP. One you have genomic locations of both your SNPs and lncRNA, it's pretty easy to find if they co-locate or not (I'm thinking of the Bedtools suite, but some tools are probably better for SNPs). Good luck and don't underestimate the power of a web research when having questions!

I do not understad "Genomic loci interaction between the SNPs and lncRNA" you said.

I guess that you may want to find out the SNPs locating in lncRNAs. Firstly, you should get and annotate these SNPs; Then, extracting some lncRNAs containing SNPs with one script file.

You can find the latest lncRNA from following link:

ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.long_noncoding_RNAs.gtf.gz

There is some ambiguity in the question you have asked. Do you mean you want to map SNP on lncRNA and associate them with some condition based on log odd ratios ?

If that is the case, you will have to be little cautious with SNPs as most of the SNP information is based on RefSeq and your lncRNA annotation is from Gencode.