Here are the codes used to generate key results in the paper.

- rmarkdown files for correlation between variable regions and ChIP/RNA/DNase signals. 
    - ChIP_VarFIRE_Shuffle_LCL20_40Kb.Rmd (correlation between FIRE and ChIP singnal is used for example. All others are the same script with different inputs.)
- R script to identify C-QTLs.
    - cqtl_lmm.R
- R script to identify FIRE/INS/DI-QTLs.
    - Rcode_LMM_FIREQTL_110918.txt (FIRE is shown as an example. All others are the same script with different inputs.)
- rmarkdown files to identify vairbale regions.
    - Variable_FIRE_region_limma_LCL20_40Kb.Rmd (FIRE is shown as an example. All others are the same script with different inputs.)
- R scripts to identify biovar regions.
    - biovar_one_chr.R
    - biovar_test_one_chr.R 
    - hic_matrix_var.R 
    - tools.R
- Power calculation scripts.
    - power_calcs.R  
    - power_v2.org