haploreg_v4.0_20151021.vcf.gz (13 GB) - all SNP-level annotations for v4.0
(NOTE: a version posted earlier had some split and corrupted rows due to improper handling of SNPs lacking hg38 positions.)
(NOTE: Zou2012 eQTL results in the v4.0 VCF were inadvertently included without a p-value threshold and should be ignored. In v4.1 these have been removed altogether from the manually curated set of eQTLS, as they are included thresholded in the GRASP hits. Instead, the v4.1 eQTL annotations listed below should be used.)
LD_AFR.tsv.gz (8.4 GB) - LD calculated on 1000 Genomes Phase 1 AFR
LD_AMR.tsv.gz (9.8 GB) - LD calculated on 1000 Genomes Phase 1 AMR
LD_ASN.tsv.gz (6.7 GB) - LD calculated on 1000 Genomes Phase 1 ASN
LD_EUR.tsv.gz (7.7 GB) - LD calculated on 1000 Genomes Phase 1 EUR
nhgri_AFR_sorted_pruned_0.2.tsv (96 kB) - NHGRI GWAS annotated as AFR with pruning results
nhgri_AMR_sorted_pruned_0.2.tsv (166 kB) - NHGRI GWAS annotated as AMR with pruning results
nhgri_ASN_sorted_pruned_0.2.tsv (268 kB) - NHGRI GWAS annotated as ASN with pruning results
nhgri_EUR_sorted_pruned_0.2.tsv (1.9 MB) - NHGRI GWAS annotated as EUR with pruning results
NOTE: These are used for v4.0 but deprecated for v4.1; a population-agnostic pruning method based on 1 MB distance is used instead for v4.1. However, the EUR pruned catalog is still used as a background for enhancer enrichment analysis in v4.1.
eqtl_metadata_v4.tsv (1 kb) - List of eQTL papers integrated for v4.0
eqtl_metadata_v4.1.tsv (1 kb) - List of eQTL papers integrated for v4.1, with methods for each
eqtls_v4.1.tsv.gz (325 MB) - Updated eQTL annotation per SNP for v4.1