Table 3 Summary GWAS statistics from the PGC bipolar disorder GWAS at 28 loci and differential expression of the “little” exon by genotype

From: Elevated expression of a minor isoform of ANK3 is a risk factor for bipolar disorder

#	Single nucleotide polymorphism					PGC 2011 BD GWAS		Norwegian sample (eQTL test)
	dbSNP RSID	Position (hg19: chr10)	Major allele	Minor allele	G1K European MAF	P-value	OR (minor)	MAF	All samples (n=705)		Excl.carriers of rs41283526*G (n=691)
									FC	p-value	FC	p-value
1	rs2288359^a	61902023	C	T	0.059	1.2E–01	1.09	0.064	1.09	5.3E–04	1.08	1.2E–03
2	rs41283526^a	61905727	A	G	0.016	3.6E–04^b	0.25^b	0.013	0.54	1.2E–08	NA^c	NA^c
3	rs12357972^a	61907907	T	C	0.048	5.5E–03	1.16	0.051	1.08	3.0E–03	1.07	5.8E–03
4	rs16914810	61913414	T	C	0.047	2.1E–02	1.98	0.05	1.08	2.0E–03	1.07	4.0E–03
5	rs2393614^a	61915955	C	T	0.319	9.6E–02	1.05	0.358	1.04	2.5E–02	1.02	8.0E–02
6	rs10509125^a	61926866	A	C	0.394	2.5E–02	1.06	0.429	1.08	4.9E–05	1.06	6.3E–04
7	rs10761473	62060382	C	G	0.078	5.6E–09	1.36	0.057	1.01	3.9E–01	1.00	5.1E–01
8	rs10509129	62071041	G	T	0.047	5.8E–09	1.36	0.041	1.04	1.3E–01	1.03	1.9E–01
9	rs1380459	62097331	C	T	0.070	3.3E–09	1.36	0.052	1.03	1.2E–01	1.02	1.8E–01
10	rs10994308	62098952	G	A	0.070	3.8E–09	1.36	0.052	1.03	1.2E–01	1.02	1.8E–01
11	rs10821736^a	62105053	C	T	0.070	1.3E–09	1.36	0.052	1.04	8.6E–02	1.03	1.3E–01
12	rs10821745^a	62136206	T	G	0.069	2.3E–09	1.35	0.054	1.04	5.7E–02	1.03	9.2E–02
13	rs10994322^a	62136279	C	T	0.069	6.7E–09	1.35	0.054	1.04	5.7E–02	1.03	9.2E–02
14	rs4948412	62146576	T	C	0.068	5.3E–09	1.35	0.054	1.04	5.7E–02	1.03	9.2E–02
15	rs3808943	62151015	C	T	0.069	4.7E–09	1.35	0.056	1.04	5.8E–02	1.03	9.4E–02
16	rs10821748	62152938	G	C	0.071	4.4E–08	1.32	0.054	1.04	5.7E–02	1.03	9.2E–02
17	rs12416380	62156154	A	G	0.069	7.5E–09	1.35	0.054	1.04	5.7E–02	1.03	9.2E–02
18	rs4948417^a	62161618	A	G	0.068	5.5E–09	1.35	0.054	1.04	5.7E–02	1.03	9.2E–02
19	rs10994336^a	62179812	C	T	0.073	4.0E–09	1.35	0.052	1.04	9.8E–02	1.03	1.5E–01
20	rs10994338^a	62181128	C	T	0.073	6.7E–09	1.34	0.052	1.04	9.8E–02	1.03	1.5E–01
21	rs9633553	62274737	T	G	0.075	5.5E–10	1.35	0.054	1.05	7.0E–02	1.04	1.1E–01
22	rs10994397^a	62279124	C	T	0.075	5.5E–10	1.35	0.054	1.05	7.0E–02	1.04	1.1E–01
23	rs12412135	62282834	C	T	0.094	4.2E–08	1.27	0.074	1.05	1.5E–02	1.05	1.9E–02
24	rs1938540	62294814	C	T	0.079	1.9E–09	1.33	0.054	1.06	2.5E–02	1.05	4.3E–02
25	rs10821792^a	62298616	C	T	0.079	2.0E–09	1.32	0.054	1.06	2.5E–02	1.05	4.3E–02
26	rs1938526	62300383	A	G	0.079	1.9E–09	1.32	0.054	1.06	2.5E–02	1.05	4.3E–02
27	rs10994415	62322034	T	C	0.074	7.0E–10	1.31	0.075	1.04	8.1E–02	1.03	1.4E–01
28	rs2154393	62326687	C	T	0.074	3.7E–09	1.29	0.076	1.04	7.2E–02	1.03	1.3E–01

Fold change (FC) is the ratio of the mean “little” exon expression for minor allele carriers to the mean for non-carriers. Tests are one-sided Wilcoxon test of higher expression of the little exon in minor allele carriers vs. non-carriers (with the exception of rs41283526, where we test lower expression in carriers)
p-values are uncorrected for multiple testing and sites significant at 5% are highlighted in bold
Samples used in the differential expression tests (eQTL test) are either all samples for which genotypes and expression are available (n = 705) or excluding those carrying the minor allele at rs41283526 (n = 691)
MAF in Norwegian sample is based on 1167 genotyped samples. Horizontal lines delineate haploblocks as determined by four gametes method on the Norwegian sample
MAF minor allele frequency, G1K 1000 genomes project (503 European individuals in G1K)
^aIndicates directly genotyped SNP (as opposed to imputed)
^bSNP minor allele frequency was too low to be genotyped or imputed with confidence in PGC GWAS. Instead, we include here the results for the Norwegian BD sample for comparison with the PGC ORs
^cNot available because of the exclusion of samples carrying rs41283526*G

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Table 3 Summary GWAS statistics from the PGC bipolar disorder GWAS at 28 loci and differential expression of the “little” exon by genotype

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