Exploring Lead loci shared between schizophrenia and Cardiometabolic traits

BMC Genomics

Table 1 Novel shared genes reaching statistical significance between SCZ and cardiovascular risk traits (BMI and TG) (conjFDR ≤ 0.05)

SNP	A1	A2	CHR	BP	conjFDR	Function	ANNOVAR	RDB	CADD	minChrState	commonChrState	Beta_BMI	SE_BMI	P_BMI	OR_SCZ	SE_SCZ	P_SCZ
Novel SNPs and Genes shared between SCZ and BMI
rs3865350	C	T	17	5,381,867	0.01.45	intronic	DERL2	6	0.393	4	4	-0.0142	0.0036	8.00 × 10^-5	1.0414	0.0097251	2.97 × 10^-5
rs9860913	A	G	3	125,137,326	0.04.48	intergenic	SNX4	5	3.826	5	15	0.0181	0.006	2.56 × 10^-³	0.93514	0.016112	3.15 × 10^-5
rs13307	G	A	2	160,659,996	0.02.28	UTR3	LY75	4	3.736	5	15	0.0129	0.0036	3.39 × 10^-4	1.0393	0.009675	6.75 × 10^-5
rs9614186	A	C	22	44,187,687	0.041	intronic	EFCAB6	4	4.526	4	15	0.0147	0.0041	3.12 × 10^-4	1.0516	0.013542	2.02 × 10^-4
Novel SNPs and Genes shared between SCZ and TG
SNP	A1	A2	CHR	BP	conjFDR	Function	Gene	RDB	CADD			Beta_TG	SE_TG	P_TG	OR_SCZ	SE_SCZ	P_SCZ
rs1472584	G	A	5	45,210,282	3.95 × 10−-2	intergenic	HCN1	7	13.21	5	15	0.0218	0.0062	5.234 × 10^-4	0.9491	0.012559	3.18 × 10^-5
rs3130544	C	A	6	31,058,340	3.79 × 10−-8	intergenic	C6orf15	3a	2.903	NA	NA	-0.043	0.0075	4.84 × 10^-10	1.1867	0.015159	1.42 × 10^-²⁹

Notes: A1 Effect allele, A2 Alter allele, CHR Chromosome number, BP Base-pair position, conjFDR Conjuctional false discovery rate, ANNOVAR Functional variant classification based on position in or outside of a gene, RBD RegulomeDB scores predicts the likelihood of regulatory functionality (lower scores, less than 3, indicate a higher likelihood), CADD Combined Annotation-Dependent depletion score, which predicts how deleterious the SNP effect is on protein structure/function (higher scores indicate more deleterious), minChrState Minimum chromatin state across 127 tissue types (lower scores indicate more open chromatin), commonChrState Most common chromatin state in 127 tissue types

ISSN: 1471-2164