Genome-wide multi-trait analysis of irritable bowel syndrome and related mental conditions identifies 38 new independent variants

Alemany, Silvia; Soler-Artigas, María; Cabana-Domínguez, Judit; Fakhreddine, Dana; Llonga, Natalia; Vilar-Ribó, Laura; Rodríguez-Urrutia, Amanda; Palacio, Judit; González-Castro, Ana María; Lobo, Beatriz; Alonso-Cotoner, Carmen; Simrén, Magnus; Santos, Javier; Ramos-Quiroga, Josep Antoni; Ribasés, Marta

doi:10.1186/s12967-023-04107-5

Table 3 Results for the 42 independent lead SNPs identified in the MTAG-IBS analysis

From: Genome-wide multi-trait analysis of irritable bowel syndrome and related mental conditions identifies 38 new independent variants

Locus	Lead SNP	CHR	A1/A2	BP	Cross-trait analysis			FRQ	Nearest Gene	Functional category	Overlap with original GWAS IBS	Overlap with previous GWAs on psychiatric traits	Overlap with previous GWAs	CADD	RDB
Locus	Lead SNP	CHR	A1/A2	BP	Beta	SE	P	FRQ	Nearest Gene	Functional category	Overlap with original GWAS IBS	Overlap with previous GWAs on psychiatric traits	Overlap with previous GWAs	CADD	RDB
1	rs301806	1	T/C	8482078	− 0.009	0.002	1.67E-09	0.58	RERE	Intronic	NO	Neuroticism	Known	0.117	4
2	rs11206127	1	A/G	53713549	− 0.009	0.002	1.42E-08	0.43	LRP8	Intronic	NO	No	Novel	0.128	6
3	rs12755507	1	T/C	176164865	0.01	0.002	8.03E-10	0.625	RFWD2	Intronic	NO	Depression	Known	6.038	4
4	rs113198479	1	A/G	191347803	− 0.02	0.004	2.48E-08	0.953	RP11-309H21.2	Intergenic	NO	No	Novel	1.241	6
5	rs72740550	1	A/G	197342380	− 0.011	0.002	6.02E-09	0.219	CRB1	Intronic	NO	Neuroticism & depression	Known	5.063	7
6	rs115962846	2	A/G	58967058	− 0.015	0.003	3.68E-08	0.912	LINC01122	ncRNA_intronic	NO	Neuroticism	Known	2.103	7
7	rs28496790	2	A/C	161950047	0.01	0.002	3.70E-09	0.708	AC009313.1	Intergenic	NO	No	Novel	6.027	5
8	rs138218528	2	T/C	212676884	0.009	0.002	2.84E-08	0.667	ERBB4	Intronic	NO	Neuroticism & depression	Known	8.481	6
9	rs62246276	3	T/G	9445173	− 0.011	0.002	2.28E-08	0.179	SETD5	Intronic	NO	No	Novel	1.944	5
10	rs67416405	3	T/C	85539234	− 0.009	0.002	8.27E-09	0.353	CADM2	Intronic	YES	No	Known	3.769	6
11	rs1729951	3	T/G	136500733	− 0.009	0.002	9.01E-09	0.389	RP11-102M11.2	Intergenic	NO	Neuroticism	Known	0.078	NA
12	rs1442129	4	A/G	90849446	− 0.009	0.002	1.22E-08	0.453	MMRN1	Intronic	NO	No	Novel	5.378	NA
13	rs77087420	4	A/G	123122856	0.018	0.003	2.64E-08	0.945	KIAA1109	Intronic	NO	No	Novel	4.579	7
14	rs12513440	5	A/G	7259853	0.01	0.002	2.73E-08	0.243	RP11-404K5.3	Intergenic	NO	No	Novel	0.327	5
15	rs3099439	5	T/C	87545318	− 0.011	0.002	1.14E-12	0.539	TMEM161B	Intronic	NO	Depression	Known	1.562	NA
16	rs4481363	5	A/C	164474719	0.009	0.001	1.01E-09	0.524	CTC-340A15.2	ncRNA_intronic	NO	Neuroticism & depression	Known	6.522	6
16	rs180928232	5	A/G	166185949	− 0.012	0.002	4.46E-08	0.149	CTB-7E3.1	Intergenic	NO	Neuroticism	Known	2.692	6
17	rs200977	6	T/C	27854301	0.015	0.002	1.04E-11	0.873	HIST1H3J	Intergenic	NO	Neuroticism & depression	Known	1.251	NA
17	rs2534664	6	A/G	31469591	0.01	0.002	2.63E-10	0.456	MICB	Intronic	NO	Depression	Known	3.484	NA
17	rs1144708	6	T/C	31710020	− 0.01	0.002	7.49E-10	0.357	MSH5:MSH5-SAPCD1	Intronic	YES	No	Known	0.372	6
18	rs12374612	6	T/C	100955752	0.009	0.001	1.02E-08	0.478	ASCC3	Downstream	NO	Neuroticism	Known	0.29	6
19	rs2189246	7	A/G	82444372	0.01	0.001	1.98E-10	0.523	PCLO	Intronic	NO	Depression	Known	1.139	7
20	rs6956352	7	A/G	109131367	0.009	0.002	1.64E-08	0.458	AC073071.1	Intergenic	NO	Depression	Known	9.195	7
21	rs4726814	7	T/C	146691924	− 0.01	0.002	1.30E-08	0.275	CNTNAP2	Intronic	NO	No	Novel	1.37	7
22	rs4478545	8	A/G	94672542	− 0.01	0.002	4.77E-09	0.285	LINC00535	ncRNA_intronic	NO	No	Novel	1.326	6
23	rs3793577	9	A/G	23737627	− 0.01	0.002	3.46E-10	0.463	ELAVL2	Intronic	NO	Neuroticism	Known	19.76	5
24	rs4744242	9	T/G	96236711	− 0.011	0.002	8.68E-13	0.336	FAM120A	Intronic	YES	Neuroticism	Known	2.858	6
25	rs10123941	9	T/C	120518162	− 0.01	0.002	3.96E-09	0.727	snoZ13_snr52	Intergenic	NO	Neuroticism	Known	1.108	6
26	rs6584631	10	T/C	106656137	− 0.01	0.002	7.23E-09	0.244	SORCS3	Intronic	NO	Depression	Known	0.167	4
27	rs4937872	11	A/G	112827715	− 0.012	0.002	7.15E-15	0.589	RP11-629G13.1	Intergenic	YES	Neuroticism	Known	0.044	6
28	rs9530139	13	T/C	31847324	− 0.011	0.002	2.11E-08	0.194	B3GALTL	Intronic	NO	Depression	Known	0.529	6
29	rs9597797	13	T/G	59183795	− 0.01	0.002	1.42E-09	0.251	CTAGE16P	Intergenic	NO	Neuroticism	Known	0.278	7
30	rs2121708	14	A/G	42146572	− 0.009	0.001	8.26E-10	0.517	LRFN5	Intronic	NO	Depression	Known	0.043	NA
31	rs35641442	14	A/G	75207263	0.009	0.002	6.65E-09	0.459	FCF1	Intergenic	NO	Neuroticism & depression	Known	11.4	7
32	rs1862743	16	A/C	60743834	− 0.009	0.001	1.08E-08	0.492	GNPATP	Intergenic	NO	No	Novel	1.06	6
33	rs11877758	18	T/G	35138110	− .,012	0.002	1.28E-13	0,692	CELF4	Intronic	NO	Neuroticism & depression	Known	2.718	7
33	rs2978362	18	T/C	32959397	− 0.008	0.001	2.65E-08	0.527	ZNF396	Intergenic	NO	Depression	Known	1.024	NA
34	rs12958048	18	A/G	53101598	0.01	0.002	4.76E-11	0,333	TCF4	Intronic	NO	Neuroticism	Known	2,08	5
34	rs17410557	18	T/C	50776391	− .,009	0.002	1.13E-08	0,606	DCC	Intronic	NO	Neuroticism & depression	Known	4.502	7
35	rs2111530	19	A/G	31891006	− 0.009	0.002	9.47E-09	0.602	AC007796.1	ncRNA_intronic	NO	No	Novel	17.04	7
36	rs2024568	20	T/C	44732089	0.011	0.002	1.52E-10	0.246	RPL13P2	Intergenic	NO	Neuroticism & depression	Known	0.149	6
37	rs11090039	22	A/G	41496800	0.012	0.002	2.87E-13	0.284	EP300	Intronic	NO	Neuroticism	Known	9.707	5

Overlap with previous GWAS was examined by identifying genome-wide significant SNPs within ± 5000 kb in the MTAG genome-wide significant for IBS and original GWAS genome-wide significant SNPs for each trait (i.e. neuroticism, depression and anxiety). If there were overlapping SNPs within this distance, they were considered independent signal if r² > 0.2. The independent signals identified (indicated as novel) were further confirmed using conditonal analysis
CHR chromosome; A1 effect allele with respect to the Beta; A2 alternate allele; BP base pair position Genome Reference Consortium Human Build 37 (GRCh37); SE standard error; FRQ frequency of the A1; CADD Combined Annotation Dependent Depletion score; RDB RegulomeDB score

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ISSN: 1479-5876

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