Table 3.

Genomic loci jointly associated with Parkinson’s disease (PD) and schizophrenia (SCZ) at conjunctional FDR<0.05

Locus	Chr	Lead SNP	A1/A2	Nearest Gene	Functional category	P-value PD	Z-score PD	P-value SCZ	Odds ratio SCZ	conjFDR
1	1	rs302714#	A/C	RERE	ncRNA_intronic	4.23E-06	4.60	2.37E-08	0.94	3.16E-03
2	4	rs13107325	T/C	SLC39A8	exonic	6.96E-08	−5.39	1.54E-12	1.16	7.43E-05
3	4	rs62333164	A/G	CLCN3	intronic	1.09E-04	−3.87	2.85E-05	1.05	3.20E-02
4*	6	rs9468195	A/G	RSL24D1P1	intergenic	1.51E-09	−6.04	5.88E-10	1.08	4.49E-06
5*	8	rs2979160	A/G	SGK223	intergenic	2.96E-06	−4.67	2.39E-06	0.95	4.11E-03
6	8	rs4921739#	T/C	ZDHHC2	intronic	6.20E-06	−4.52	1.24E-06	0.93	4.27E-03
7	10	rs79780963	T/C	NT5C2	intronic	2.12E-04	−3.70	2.79E-16	0.85	4.97E-02
8	11	rs3802921	T/C	IGSF9B	UTR3	6.88E-09	−5.79	2.40E-06	0.94	4.13E-03
9	12	rs73228032	A/C	HIP1R	intronic	4.95E-05	−4.06	6.51E-05	0.93	3.90E-02

The most strongly associated SNPs in independent genomic loci shared between SCZ and PD at conjFDR<0.05 after merging regions < 250 kb apart into a single locus. The table presents chromosomal position (Chr), nearest gene and functional category, as well as p-values and effect sizes (odds ratios or z-scores) from the original summary statistics on SCZ and PD. The effect sizes are given with reference to allele 1 (A1). Novel PD risk loci are labeled with^#.

^*The significant shared signals in the major histocompatibility complex region (chr6:25119106–33854733; locus 4) and chromosomal region 8p23.1 (chr8:7200000–12500000; locus 5) are represented by only one independent lead SNP each given their extended LD. For more details and a list of all candidate variants in these loci, see Supplemental Table 7. See Supplemental Table 8 for genes mapped to these loci.