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. 2021 Nov 3;37(7):110020. doi: 10.1016/j.celrep.2021.110020

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© 2021 The Author(s)

Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

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Colocalizations between COVID-19 GWAS and tissue eQTL signals

For each of the 11 fine-mapped loci, four panels are presented: (1) GWAS p values for indicated COVID-19 phenotype; (2) eQTL p values for indicated gene; (3) posterior probability of colocalization of each variant (coloc PP; calculated using coloc) and color-coded based on linkage disequilibrium in individuals of European descent (r²) calculated using LDlinkR (Myers et al., 2020); and (4) location of gene in locus. The p values of all variants tested in the GWAS and eQTL studies are shown; however, only variants tested in both studies were used for colocalization.

(A) Locus 6:40997035-42005196, phenotype B2 GWAS (B2_ALL_leave_23andme), and FOXP4 eQTL in lung.

(B) Locus 6:32555355-33555355, phenotype A2 GWAS (A2_ALL_leave_23andme), and HLA-DPA2 eQTL in brain cerebellum.

(C) Locus 19:4184642-5224734, phenotype B2 GWAS (B2_ALL_eur_leave_ukbb_23andme), and PTPRS eQTL in colon sigmoid.

(D) Locus 1:154605882-155673527, phenotype C2 GWAS (C2_ALL_eur_leave_23andme), and FAM189B eQTL in heart atrial appendage; although this signal is severity associated, only the C2 phenotype colocalized with an eQTL.

(E) Locus 6:30620729-31621958, phenotype B2 GWAS (B2_ALL_leave_UKBB_23andme), and TCF19 eQTL in lung.

(F) Locus 19:9927721-10977067, phenotype A2 GWAS (A2_ALL_eur_leave_23andme), and TYK2 eQTL in adrenal gland.

(G) Locus 9:135628546-136796530, phenotype C2 GWAS (C2_ALL_leave_23andme), and ABO eQTL in adipose visceral omentum.

(H) Locus 12:112850796-113925679, phenotype B2 GWAS (B2_ALL_leave_23andme), and OAS1 eQTL in adipose subcutaneous.

(I) Locus 3:100646362-102035347, phenotype C2 GWAS (C2_ALL_eur_leave_23andme), and PDCL3P4 eQTL in cerebellum; since the FOXP4 locus was associated with non-European individuals, LD is shown for East Asians.

(J) Locus 21:34089811-35134878, phenotype B2 GWAS (B2_ALL_eur_leave_ukbb_23andme), and IFNAR2 eQTL in muscle skeletal.

(K) Locus 17:43205356-45363133, phenotype B1 GWAS (B1_ALL_leave_23andme), and LRRC37A eQTL in pancreas.