SNP Report

Basic Info

Name	rs4650608 dbSNP Ensembl
Location	chr1:78772330 - 78772330(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.228634
No. of Studies	3 (Positive: 2; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 3)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Andreassen OA, 2013	T/C		Conditional FDR; SCZ loci given BD: FDR=0.028 for SCZ and BD...... Conditional FDR; SCZ loci given BD: FDR=0.028 for SCZ and BD\|\|Conditional FDR; BD loci given SCZ: P-value=0.001, FDR=0.64629, FDR=0.0425 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.043 for BD and SZ, Z-score=3.289 for BD More...	To estimate the number of independent loci, we 'pruned' the ...... To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.08. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.06 with schizophrenia and bipolar disorder considered jointly. More...	Positive
Chen, D. T.,2011		T	Meta-analysis results by ancestry: European and Asian-ancest...... Meta-analysis results by ancestry: European and Asian-ancestry phase I samples: Fixed effects P-value = 1.20E-07, Random effects P-value = 9.25E-06, I²=52.26, Q test=6.28, Q test P-value = 0.099; European and Asian-ancestry phase I & phase II samples: Fixed effects P-value = 8.35E-09, Random effects P-value = 1.06E-06, I²=39.04, Q test=8.2, Q test P-value = 0.145; European-ancestry phase I samples: Fixed effects P-value = 2.10E-07, Random effects P-value = 2.29E-05, I²=61.92, Q test=5.25, Q test P-value = 0.072; European-ancestry phase I and phase II samples: Fixed effects P-value = 1.56E-08, Random effects P-value = 2.71E-06, I²=44.18, Q test=7.17, Q test P-value = 0.127 More...	The results suggest novel association findings. The results suggest novel association findings.	Positive
Ruderfer, D. M., 2013			P-value=1.22E-05 for BP, P-value=8.30E-09 for BP+SZ, Het P-v...... P-value=1.22E-05 for BP, P-value=8.30E-09 for BP+SZ, Het P-value=0.76 More...	Most significant SNP in six genome-wide significant regions....... Most significant SNP in six genome-wide significant regions. More...	Negative

SNP related genes (count: 2)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
PTGFR	prostaglandin F receptor (FP)	1p31.1	1(1/0/0)
IFI44L	interferon-induced protein 44-like	1p22.3	1(0/1/0)

SNPs in LD with rs4650608 (count: 0) View in gBrowse (chr1:78772330..78772330 )

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Ruderfer, D. M., 2013	P-value=1.77E-04 for BP, P-value=5.53E-13 for BP+SZ, Het P-value=0.85	Most significant SNP in six genome-wide significant regions.	Negative
Andreassen OA, 2013	Conditional FDR; SCZ loci given BD: P-value=0.000206, FDR=0.257, FDR=0.028 for SCZ and BD\|\|Conditional FDR; BD loci given SCZ: FDR=0.0425 for BD and SCZ\|\|Conjunction FDR; pleiotropic loci in SCZ and BD: FDR=0.043 for BD and SZ, Z-score=3.711 for SZ	To estimate the number of independent loci, we 'pruned' the associated SNPs (removed SNPs with linkage disequilibrium (LD)>0.2), and identified a total of 58 independent loci with a significance threshold of conditional FDR<0.08. This SNP is with conditional FDR<0.05 in schizophrenia given association with bipolar disorder after 'pruning'. This SNP is with conjunction FDR<0.06 with schizophrenia and bipolar disorder considered jointly.	Positive

Overlap with MDD from cross-disorder studies (count: 0)