Worldwide distribution of genetic factors related to severity of COVID-19 infection

Figures & data

Figure 1. Chromosome location, SNP identification/nearby gene(s), and minor allele frequency distribution of the nine SNPs associated with COVID-19 severity in the main geographical regions included in the 1000 Genomes Project Reference Panel.

Table 1. Minor allele frequencies and gene information for the nine top SNPs associated to COVID-19 severity in Cruz et al. (2022) in each of the five geographical regions included in the 1000 Genomes Project Consortium.

SNP	Change	Gene Consequence	Gene  (or nearby)	Global	Africa	East Asia	Europe	South Asia	America
rs115679256	G > A	NONE	LIMD1	0.0144	0.0015	0.0010	0.0457	0.009	0.020
rs17763742	A > G	LOC107986082: Non Coding Transcript Variant	LZTFL1	0.0827	0.0038	0.0099	0.0805	0.296	0.042
rs35477280	G > A	FYCO1: Intron Variant	FYCO1	0.1072	0.0045	0.0040	0.1203	0.374	0.058
rs4443214	T > C	LOC105377067: Intron Variant	XCR1	0.2270	0.4380	0.0456	0.1173	0.313	0.127
rs115102354	A > G	LOC105377067: Intron Variant	CCR3	0.0172	0.0015	0.0000	0.0477	0.024	0.019
rs10813976	A > G	NONE	AQP3	0.1801	0.1097	0.1696	0.1958	0.262	0.192
rs1230082	G > C	ARHGAP27: Intron Variant	ARHGAP27	0.5651	0.4705	0.4405	0.6968	0.642	0.627
rs77127536	G > A	NONE	UPK1A/  ZBTB32	0.1999	0.1740	0.2798	0.1809	0.214	0.141
rs17860169	A > G	IFNAR2: Intron Variant	IFNAR2	0.3986	0.1936	0.5774	0.3330	0.521	0.451

Figure 2. Boxplots of LD scores per (A) main geographical regions (AFRICA: ACB, ASW, ESN, GWD, LWK, MSL, YRI, EUROPE: CEU, FIN, GBR, IBS, TSI; SOUTH ASIA: BEB, GIH, ITU, PJL, STU; EAST ASIA: CDX, GHB, CHS, JPT, KHV; AMERICA: CLM, MXL, PEL, PUR) and (B) populations within regions (red = Africa; yellow = Europe; green = South Asia; Blue = East Asia; purple = America).

Figure 3. Boxplots of polygenic risk scores per (A) regions (EUR = Europe; SAS = South Asia; AMR = America), and (B) populations within regions (yellow = Europe; Green = South Asia; Purple = America).

Cruz R, Diz-de Almeida S, López de Heredia M, Quintela I, Ceballos FC, Pita G, Lorenzo-Salazar JM, González-Montelongo R, Gago-Domínguez M, Sevilla Porras M. 2022. Novel genes and sex differences in COVID-19 severity. Hum Mol Genet. 31(22):3789–3806. doi: 10.1093/hmg/ddac132.

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