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QTL Datasets
Andrew Elmore edited this page Nov 21, 2024
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1 revision
Summary of datasets to collect:
| Tissue | Molecular Trait | Study | Link | Original format | BESD formatted | Genome build | N |
|---|---|---|---|---|---|---|---|
| Whole blood | Single-cell eQTL | OneK1K | https://onek1k.org/ | tsv | No | GRCh37/hg19 | 982 |
| Whole blood | Bulk eQTL | eQTLGen phase I | https://www.eqtlgen.org/phase1.html | Original formal | Yes | GRCh37.p10 | 31684 |
| Whole blood | Single-cell eQTL | eQTLGen phase II | https://www.eqtlgen.org/sc/ | Multiple studies - in stimulated condition - do we want these? | No | X | X |
| Whole blood | Methylation-QTL | GoDMC | http://mqtldb.godmc.org.uk/downloads | csv | No | hg19/build37 | 27750 |
| Whole blood | Protein-QTL | UKB-PPP | https://registry.opendata.aws/ukbppp/ | tar | In progress | hg38 | 54219 |
| Whole blood | Splice-QTL | GTEx | https://yanglab.westlake.edu.cn/software/smr/#eQTLsummarydata | BESD (Yang Lab data) | Yes | hg19 | 670 |
| Brain - Basalganglia (Eur) | Bulk cis-eQTL | MetaBrain | https://download.metabrain.nl/files.html | txt | No | GRCh38 | 208 |
| Brain - Cerebellum (Eur) | Bulk cis-eQTL | MetaBrain | https://download.metabrain.nl/files.html | txt | No | GRCh38 | 492 |
| Brain - Cortex (Eur) | Bulk cis-eQTL | MetaBrain | https://download.metabrain.nl/files.html | txt | No | GRCh38 | 2683 |
| Brain - Hippocampus (Eur) | Bulk cis-eQTL | MetaBrain | https://download.metabrain.nl/files.html | txt | No | GRCh38 | 168 |
| Brain - Spinalcord (Eur) | Bulk cis-eQTL | MetaBrain | https://download.metabrain.nl/files.html | txt | No | GRCh38 | 108 |
| Brain - Cortex (Afr) | Bulk cis-eQTL | MetaBrain | https://download.metabrain.nl/files.html | txt | No | GRCh38 | 319 |
| Brain - Cortex (Eas) | Bulk cis-eQTL | MetaBrain | https://download.metabrain.nl/files.html | txt | No | GRCh38 | 208 |
| Brain - Cortex (Eur) | Bulk cis-eQTL | BrainMeta v2 | https://yanglab.westlake.edu.cn/software/smr/#eQTLsummarydata | BESD (Yang Lab data) | Yes | hg19 | 2443 |
| Brain - Cortex (Eur) | Bulk trans-eQTL | BrainMeta v2 | https://yanglab.westlake.edu.cn/software/smr/#eQTLsummarydata | BESD (Yang Lab data) | Yes | hg19 | 2443 |
| Brain - 10 Brain regions | Bulk cis-eQTL | BrainMeta v1 | https://yanglab.westlake.edu.cn/software/smr/#eQTLsummarydata | BESD (Yang Lab data) | Yes | hg19 | 1194 |
| Multiple tissues | Bulk eQTL | GTEx | https://yanglab.westlake.edu.cn/software/smr/#eQTLsummarydata | BESD (Yang Lab data) | Yes | hg19 | X |
| Multiple tissues | Bulk splice-QTL | GTEx | https://yanglab.westlake.edu.cn/software/smr/#eQTLsummarydata | BESD (Yang Lab data) | Yes | hg19 | X |
| Multiple tissues | Bulk cis-mQTL | GTEx | https://www.nature.com/articles/s41588-022-01248-z#data-availability | ??? | X | X | X |
| Immune Cell QTLs | DICE | https://dice-database.org/downloads#eqtl_download | ??? | X | X | X |