├── .gitignore ├── LICENSE ├── README.md ├── TODO.txt ├── about.md ├── archive.R ├── data ├── example │ ├── PCSK9_Adipose_Visceral_Omentum.tsv │ ├── PCSK9_Coronary_Heart_Disease_Nikpay_2015.tsv │ ├── PHACTR1_Artery_Aorta.tsv │ ├── PHACTR1_Artery_Coronary.tsv │ ├── PHACTR1_Artery_Tibial.tsv │ ├── PHACTR1_Coronary_Heart_Disease_Nikpay_2015.tsv │ ├── PHACTR1_Coronary_Heart_Disease_Nikpay_2015_batch.tsv │ ├── PHACTR1_all_tissues.tsv │ ├── archive │ │ ├── GWAS_Asthma_Moffatt_2010_chr2_101973286_103971063.tsv │ │ ├── GWAS_Asthma_Moffatt_2010_chr2_chr9_chr22.tsv │ │ ├── eQTL_Cells_EBV_transformed_lymphocytes_GTEx_2017_chr2_101972000_103972000.tsv │ │ ├── eQTL_Lung_GTEx_2017_IL18R1.tsv │ │ └── eQTL_Lung_GTEx_2017_IL18R1_IL33_IL2RB.tsv │ └── batch_region.txt ├── gencode │ └── gencode.v19.genes.v6p.hg19.bed ├── population │ ├── AFR.txt │ ├── AMR.txt │ ├── EAS.txt │ ├── EUR.txt │ └── SAS.txt ├── study_info │ └── study_info.txt └── ukbb │ └── UKBB_ICD10_mapping.tsv ├── global.R ├── init.js ├── locuscompare.R ├── logo.png ├── misc └── wiki-batch_query.txt ├── server.R ├── ui.R └── utils ├── archive ├── make_input.R └── save_to_mysql.R ├── colocalization ├── SYPL2.txt ├── compare_smr_and_ecaviar.R ├── gtex_sample_size.sh ├── plot_locuscompare.R ├── sample_size_vs_clpp.R └── smr_eda.R ├── count_gtex_samples └── count.sh ├── count_trait └── count_trait.R ├── etc ├── PHACTR1_eQTL_pval.R ├── PHACTR1_expression.R ├── concatenate_PHACTR1.R └── selecct_PHACTR1.sql ├── fig1 ├── fig1.R ├── fig1_v2.R ├── gwas_cad_nelson_2017.R ├── gwas_t2d_zhao_2017.R └── shared.R ├── format ├── GWAS_Coronary-Artery-Disease_Nelson_2017.R └── GWAS_Type-2-Diabetes_Zhao_2017.R ├── googledrive └── clean.R ├── mysql ├── calc_LD.R ├── coloc2mysql.R ├── correct_trait_names.R ├── failed_gwas.txt ├── gencode2mysql.R ├── gtex2mysql.R ├── gtex_sex_2_mysql.R ├── gtex_trait_table.R ├── gtex_v7_2_mysql.R ├── gtex_v7_trait_table.R ├── gwas2mysql.R ├── gwas_trait_table.R ├── ld2mysql.R ├── ld2mysql.sh ├── 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