TABLE 4.

Genetic variants, associated with clinical subphenotypes.

Chr	Pos (hg38)	Ref	Alt	Variant	Trait	Cohort	Model	Association	p-value	Gene	Strand	Variant biological function
8	32614509-32614510	TT	del	NC_000008.11: g.32614509_32614510del	Drug treatment response	Depression	Binomial logistic regression	Absence of response on the 28th day assessed by HDRS-17 is associated with allele “del”	3.22E-04	NRG1	F	Intronic, no obvious function
	32648114	G	C	rs35641374	Time to recurrence of a depressive episode	Cross disorder	Linear regression	Longer intervals between depressive episodes are associated with allele C	3.14E-06			Missense in five transcripts, Val > Leu, likely benign for protein function
					Time to recurrence of a depressive episode	Bipolar		Longer intervals between depressive episodes are associated with allele C	4.37E-07
					Time to recurrence of an episode	Bipolar		Longer intervals between episodes of any type are associated with allele C	3.43E-04
10	22541913	C	T	rs61731109	Drug treatment response	Depression	Binomial logistic regression	absence of response on the 28th day assessed by HDRS-17 is associated with allele T (passed FDR, but not Bonferroni correction for multiple comparisons)	1.11E-03	PIP4K2A	R	Synonymous in all transcripts; allele A (reverse complement) may affect splicing (†HumanSplicingFinder)
	22573353	T	C	rs10508649	Drug treatment response	Depression	Binomial logistic regression	Absence of response on the 28th day assessed by CGI-I scale is associated with allele C	9.43E-04			Synonymous in all transcripts; allele G (reverse compliment) may affect splicing (†HumanSplicingFinder); found within enhancer GH10J022572 that regulates expression of PIP4K2A (†GeneHancer)
					Time to recurrence of a manic or mixed episode	Bipolar	Linear regression	Longer intervals between manic or mixed episodes are associated with allele C	3.09E-04
X	114727001	A*	G	rs2248440	Severity	Depression	Ordinal logistic regression	Higher severity of depression is associated with allele A	3.00E-03	HTR2C	F	Intronic; allele A decreases expression of IL13RA2 in putamen (†GTEx)

Chr, chromosome; pos, position in the human genome; ref, reference allele; alt, alternate allele; ^†used algorithms; * minor allele.