African Functional Genomics Resource (AFGR)

The African Functional Genomics Resource includes RNA-seq, expression QTLs (eQTLs), and splicing QTLs (sQTLs) on all 593 individuals, and ATAC-seq and chromatin accessibility QTLs (caQTLs) on a representative 100 individual subset. The populations and their numbers are represented in the map below. eQTLs are defined as SNP-transcript pairs; sQTLs are SNP-splice junction pairs; caQTLs are SNP-chromatin region pairs.

Download QTL Data

All QTL summary statistics files will be available in tabixed format in the AFGR Dropbox

eQTLs:

AFGR eQTLs

• ESN
• GWD
• LWK
• MSL
• YRI
• MKK
• Meta-analysis

GEUVADIS eQTLs

GEUVADIS eQTLs called and meta-analyzed using the same pipeline as AFGR

• CEU
• FIN
• GBR
• TSI
• EUR (bulk-called eQTLs across CEU, FIN, GBR, and TSI)
• Meta-analysis (meta-analysis of CEU, FIN, GBR, and TSI eQTLs)
• YRI

sQTLs: AFGR sQTLs

• ESN
• GWD
• LWK
• MSL
• YRI
• MKK
• Meta-analysis

caQTLs: AFGR caQTLs

• AFR (called in bulk using ATAC-seq data from 100 samples spanning all 6 population groups)

Access RNA-seq and ATAC-seq Data

The RNA-seq and ATAC-seq tracks will be available at ENCODE soon.