This is an attempt for an automated way to download and reproduce fuma reference data.
Here is the table reformatted to markdown:
| Category | Name | Description | Last accessed | Link |
|---|---|---|---|---|
| Reference Variants | dbSNP 146 | Map rsID of input files to dbSNP build 146 | 18-Mar-16 | link |
| Reference Genome | 1000 Genomes Project Phase3 | Compute MAF and r2 for each available population | 25-Apr-16 | link |
| Functional annotations of SNPs | CADD v1.3 | Deleteriousness score of variants | 09-Jul-16 | link |
| Functional annotations of SNPs | RegulomeDB | Score of regulatory variants | 16-Feb-16 | link |
| Functional annotations of SNPs | 15-core chromatin state | Chromatin states of genomic region in 127 tissue/cell types | 15-May-16 | link |
| Functional annotations of SNPs | GWAS catalog | Known trait associated variants | 05-Oct-16 | link |
| eQTLs | GTEx v6 | cis-eQTLs of 44 tissue types | 16-Mar-16 | link |
| eQTLs | Blood eQTL Browser | cis-eQTLs of blood cell | 06-Jun-16 | link |
| eQTLs | BIOS QTL Browser | cis-eQTLs of blood cell | 07-Oct-16 | link |
| eQTLs | BRAINEAC | cis-eQTLs of 10 brain regions | 09-Sep-16 | link |
| HiC | GSE87112 | HiC data for 14 tissue types and 7 cell lines | 24-Apt-17 | link |
| Regulatory elements | Roadmapc epigenomics project | Enhancer, promoter and dyadic enhancer/promoter regions in 111 epigenomes | 24-Apt-17 | link |
| Gene score | pLI | Probability of being loss-of-function intolerance | 24-Apt-17 | link |
| Gene score | ncRVIS | Non-coding residual variation intolerance score | 24-Apt-17 | link |
| Gene expression | GTEx v6 | Normalized gene expression (RPKM: Read Per Kilo base per Million) for 53 tissue types | 16-Mar-16 | link |
| Gene sets | MsigDB v5.2 | Curated pathways and gene sets | 26-Dec-16 | link |
| Gene sets | WikiPathways | Curated pathways | 22-Apr-16 | link |
| Tools | ANNOVAR | Variant annotation tool | 11-Feb-16 | link |
| Tools | MAGMA v6.0 | Software for gene-based test and gene-set analyses of GWAS | 17-Jan-17 | link |