. Author manuscript; available in PMC: 2019 Aug 26.

Published in final edited form as: Ann Neurol. 2018 Aug 26;84(1):117–129. doi: 10.1002/ana.25274

TABLE 4.

Expression Quantitative Trait Locus Analyses

Expression Outcome	SNP	Dataset	β	SE	P
Total SNCA	rs2870004	CAGEseq	0.095	0.11	0.40
		RNAseq	−0.018	0.16	0.91
		qPCR	0.052	0.20	0.80
	rs356182	CAGEseq	0.276	0.10	0.0088
		RNAseq	−0.191	0.14	0.17
		qPCR	0.179	0.20	0.38
	rs763443	CAGEseq	−0.021	0.12	0.86
		RNAseq	0.016	0.09	0.86
		qPCR	−0.019	0.18	0.91
NM_000345	rs2870004	CAGEseq	0.033	0.11	0.77
		RNAseq	−0.070	0.16	0.66
		qPCR	−0.036	0.20	0.86
	rs356182	CAGEseq	0.086	0.10	0.40
		RNAseq	−0.103	0.14	0.46
		qPCR	−0.176	0.20	0.38
	rs763443	CAGEseq	−0.125	0.09	0.17
		RNAseq	−0.024	0.12	0.84
		qPCR	0.018	0.18	0.92
NM_001146054	rs2870004	CAGEseq	0.283	0.12	0.018
		RNAseq	−0.033	0.16	0.83
		qPCR	0.179	0.20	0.36
	rs356182^a	CAGEseq	0.445	0.11	7.0e-05
		RNAseq	0.295	0.14	0.034
		qPCR	0.559	0.19	0.0055
	rs763443	CAGEseq	0.040	0.09	0.67
		RNAseq	0.211	0.12	0.08
		qPCR	−0.084	0.17	0.63
NM_001146055	rs2870004	CAGEseq	−0.103	0.11	0.33
		RNAseq	0.051	0.16	0.75
		qPCR	−0.379	0.19	0.046
	rs356182	CAGEseq	0.108	0.10	0.27
		RNAseq	−0.313	0.14	0.024
		qPCR	0.128	0.19	0.49
	rs763443	CAGEseq	0.087	0.09	0.31
		RNAseq	−0.041	0.12	0.73
		qPCR	0.259	0.16	0.12
NM_001146054 fraction of total SNCA	rs2870004	CAGEseq	0.336	0.11	0.0020
		RNAseq	−0.029	0.15	0.85
		qPCR	0.156	0.19	0.42
	rs356182^a	CAGEseq	0.439	0.10	1.7e-5
		RNAseq	0.494	0.13	2.9e-4
		qPCR	0.584	0.19	0.0032
	rs763443	CAGEseq	0.048	0.09	0.58
		RNAseq	0.263	0.12	0.024
		qPCR	−0.084	0.17	0.62
CSF α−synuclein	rs2870004	PPMI	0.071	0.03	0.038
	rs356182^a		0.077	0.03	0.015
	rs763443		−0.004	0.03	0.89

The table shows results from linear regression of risk variant association with mRNA levels and CSF α-synuclein. For comparison of effect sizes across gene expression analysis methods, mRNA expression levels have been converted to z scores. Effect alleles correspond to Table 1.

Significant associations, see main text.

CAGEseq = cap analysis gene expression sequencing; CSF = cerebrospinal fluid; PPMI = Parkinson’s Progression Marker Initiative; qPCR = quantitative polymerase chain reaction; RNAseq = RNA sequencing; SE = standard error; SNP = single nucleotide polymorphism.