Table 2.

Summary of G2G analysis results.

Locus	EBV dataset	EBV outcome	SNP	Chr	OR**	p	Finemapped SNP	Finemapped probability	Effect allele	EAF	n	Gene	Consequence type
2	Gene (binary, variants < 1 sample)	BALF5	rs2950922*	8	1.30739	4.2E−12	TRUE	0.13317	G	0.10821	268	UNC5D***	Intron_variant
3	Gene (binary, variants < 1 sample)	BBRF1	rs62124869*	2	1.29103	4.3E−11	TRUE	0.71847	C	0.0541	268	LINC01830	Non_coding_transcript_variant
1	Amino acid (binary)	BRLF1:p.Lys316Glu	rs7808072*	7	1.41346	6.8E−11	FALSE		T	0.06762	244
1	Amino acid (binary)	BRLF1:p.Lys316Glu	rs6466720	7	1.42464	7.7E−11	TRUE	0.04783	G	0.06967	244

Top SNP and/or fine-mapped SNP per locus represented with: EBV dataset, EBV outcome, chromosome, SNP identifier, odds ratio, p value, whether this SNP is a top SNP or a fine-mapped SNP, the causal probability from FINEMAP, effect allele, effect allele frequency, sample size, corresponding gene, variant consequence, associated eQTL gene, associated eQTL associated eQTL gene and p value in GTEx (from https://gtexportal.org/home/)⁷¹. See Supplementary Table S1 for detailed information about all 25 variants and Supplementary Table S2 for fine-mapping results.

*SNP with locus-wide lowest p value.

**Odds ratio (exp(b) for logistic mixed effects model) in SHCS.

***Gene and tissue of eqtl association (p value of association), from GTEX:

UNC5D in Esophagus_Muscularis (p = 1.15243e−13), UNC5D in Esophagus_Gastroesophageal_Junction (p = 2.61983e−05).