Table 3.

Genome-wide significant SNPs associated with GORD, PG₊M, and IBS in the UK Biobank.

Digestion phenotypes	SNP*	CHR.	BP	A1/A2	A1 frequency	OR†	P	Nearby genes‡	Digestive diseases pleiotropy§	Mental health pleiotropy§
GORD	rs77968610	12	78532859	T/C	0.88	0.95	2.8E−08	NAV3	–	–
	rs32546	5	13205087	C/T	0.60	1.04	3.5E−08	–	–	–
	rs10891491	11	112898216	C/T	0.89	0.95	4.1E−08	NCAM1	–	Depressive symptoms, depressed affect
PG+M	rs12532051	7	147806981	C/G	0.96	1.08	1.2E−09	CNTNAP2	–	–
	rs9800013	5	542023	A/G	0.77	0.96	2.9E−09	–	UC	–
	rs149140438	22	32277882	A/C	0.98	0.90	9.9E−09	DEPDC5	–	–
	rs72915655	2	194001113	T/C	0.83	1.04	1.1E−08	–	–	ASD, Anorexia nervosa, SCZ, etc.
	rs3863241	8	73890335	C/T	0.47	0.97	1.9E−08	–	–	–
	14:103333187	14	103333187	AAC/A	0.76	0.97	4.3E−08	TRAF3	–	–
IBS	rs7947502	11	112909396	C/T	0.41	1.05	2.5E−08	NCAM1	–	Depressive symptoms, depressed affect
	rs2523599	6	31241092	C/G	0.39	0.95	4.4E−08	HLA-C	#	#

^*Locus zoom plot for SNPs are in Supplementary Figs. 5–7. Supplementary Table 4 lists genome-wide significant SNPs associated with GORD and PG₊M that have been previously reported to be associated with gastroesophageal reflux²⁰. 

^†Odds ratio (OR) is for risk of A1 allele compared to A2 allele.

^‡We note that we do not have direct evidence to support the nearby genes as causal genes, except when linked to gene expression (see Summary data-based Mendelian randomization analysis at the Links to gene expression, eQTLs, and mQTLs section).

^§We only annotated SNPs if there are SNPs reported associated with either mental health-related traits or digestive diseases from GWAS Catalog in linkage disequilibrium with our UKB digestion SNPs (see “Methods” section and Supplementary Data 1 for detailed description). “#” represents that SNP is within MHC region. For SNPs within MHC region see Supplementary Data 1 for details given the complexity of MHC region.

ASD Autism spectrum disorder, SCZ Schizophrenia, UC Ulcerative colitis.