A Role for Noncoding Variation in Schizophrenia

Abstract

A large portion of common variant loci associated with genetic risk for schizophrenia reside within noncoding
sequence of unknown function. Here, we demonstrate promoter and enhancer enrichment in schizophrenia variants associated with expression quantitative trait loci (eQTL). The enrichment is greater when functional annotations derived from the human brain are used relative to peripheral tissues. Regulatory trait concordance analysis ranked genes within schizophrenia genome-wide significant loci for a potential functional role, based on colocalization of a risk SNP, eQTL, and regulatory element sequence. We identified potential physical interactions of noncontiguous proximal and distal regulatory elements. This was verified in prefrontal cortex and -induced pluripotent stem cell–derived neurons for the L-type calciumchannel (CACNA1C) risk locus. Our findings point to a functional link between schizophrenia-associated noncoding SNPs and 3D genome architecture associated with chromosomal loopings and transcriptional regulation in the brain.

Full text

Article
A Role for Noncoding Variation in Schizophrenia
Graphical Abstract
Highlights
Schizophrenia SNPs are enriched for eQTLs and cis-regulatory
elements
The enrichment is greater for enhancers in fetal and adult brain
tissue
Schizophrenia risk SNPs participate in long-range promoter-
enhancer interactions
CACNA1C variants are associated with transcriptional regula-
tion in the brain
Authors
Panos Roussos, Amanda C. Mitchell, ...,
Schahram Akbarian, Pamela Sklar
Correspondence
panagiotis.roussos@mssm.edu (P.R.),
pamela.sklar@mssm.edu (P.S.)
In Brief
Roussos et al. find that schizophrenia risk
variants are enriched for alleles that affect
gene expression and lie within promoters
or enhancers. For the L-type calcium
channel (CACNA1C), the risk variant is
associated with transcriptional regulation
in the brain and is positioned within an
enhancer sequence that physically inter-
acts though chromosome loops with the
promoter region of the gene.
Accession Numbers
GSE62391
Roussos et al., 2014, Cell Reports 9, 1–13
November 20, 2014 ª2014 The Authors
http://dx.doi.org/10.1016/j.celrep.2014.10.015

Cell Reports
Article
A Role for Noncoding Variation in Schizophrenia
Panos Roussos,
1,2,3,4,5,20,
*Amanda C. Mitchell,
1,4,6,20
Georgios Voloudakis,
1,4,6
John F. Fullard,
1,4
Venu M. Pothula,
1,4,6
Jonathan Tsang,
1
Eli A. Stahl,
1,2,3
Anastasios Georgakopoulos,
1
Douglas M. Ruderfer,
1,2,3
Alexander Charney,
1,2,3
Yukinori Okada,
7,8
Katherine A. Siminovitch,
9,10,11
Jane Worthington,
12,13
Leonid Padyukov,
14
Lars Klareskog,
14
Peter K. Gregersen,
15
Robert M. Plenge,
16,17,18
Soumya Raychaudhuri,
16,17,18,19
Menachem Fromer,
1,2,3
Shaun M. Purcell,
1,2,3
Kristen J. Brennand,
1,4,6
Nikolaos K. Robakis,
1,4,6
Eric E. Schadt,
2,3
Schahram Akbarian,
1,4,6,21
and Pamela Sklar
1,2,3,4,6,21,
*
1
Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
2
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
3
Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
4
Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
5
James J. Peters VA Medical Center, Mental Illness Research Education and Clinical Center (MIRECC), 130 West Kingsbridge Road, Bronx,
NY 10468, USA
6
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
7
Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental
University, Tokyo 230-0045, Japan
8
Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
9
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
10
Toronto General Research Institute, Toronto, ON M5G 2M9, Canada
11
Department of Medicine, University of Toronto, Toronto, ON M5S 2J7, Canada
12
Arthritis Research UK Centre for Genetics and Genomics, Musculoskeletal Research Centre, Institute for Inflammation and Repair,
Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9NT, UK
13
National Institute for Health Research, Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals
National Health Service Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9NT, UK
14
Rheumatology Unit, Department of Medicine (Solna), Karolinska Institutet, Stockholm 171 76, Sweden
15
The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, NY 11030, USA
16
Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
17
Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
18
Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
19
NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health
Sciences Centre, Manchester M13 9NT, UK
20
Co-first author
21
Co-senior author
*Correspondence: panagiotis.roussos@mssm.edu (P.R.), pamela.sklar@mssm.edu (P.S.)
http://dx.doi.org/10.1016/j.celrep.2014.10.015
This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).
SUMMARY
A large portion of common variant loci associated
with genetic risk for schizophrenia reside within non-
coding sequence of unknown function. Here, we
demonstrate promoter and enhancer enrichment in
schizophrenia variants associated with expression
quantitative trait loci (eQTL). The enrichment is
greater when functional annotations derived from
the human brain are used relative to peripheral tis-
sues. Regulatory trait concordance analysis ranked
genes within schizophrenia genome-wide significant
loci for a potential functional role, based on colocal-
ization of a risk SNP, eQTL, and regulatory element
sequence. We identified potential physical interac-
tions of noncontiguous proximal and distal regula-
tory elements. This was verified in prefrontal cortex
and -induced pluripotent stem cell–derived neurons
for the L-type calcium channel (CACNA1C) risk locus.
Our findings point to a functional link between
schizophrenia-associated noncoding SNPs and 3D
genome architecture associated with chromosomal
loopings and transcriptional regulation in the brain.
INTRODUCTION
A recent multistage genome-wide association study (GWAS) in
schizophrenia (SCZ) identified 22 linkage disequilibrium (LD)-in-
dependent loci that reached genome-wide significance (Ripke
et al., 2013). The majority of identified SNPs reside within non-
coding regions of genes or in intergenic regions. Furthermore,
the regions were frequently large and often contained multiple
implicated SNPs due to local LD patterns. In order to be able
to understand these associations mechanistically, it is important
to develop strategies for honing in on regions and SNPs more
likely to have functional effects. Thus, the elucidation of the func-
tion of noncoding disease-associated loci is an important next
step toward the development of testable hypotheses regarding
biological processes involved in the pathogenesis of SCZ.
Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors 1
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

Across many phenotypes, noncoding GWAS risk loci are
involved in the regulation of transcriptional activity and demon-
strate enrichment for expression quantitative trait loci (Nicolae
et al., 2010; Richards et al., 2012; Zhong et al., 2010) and
cis-regulatory elements (CREs) (Degner et al., 2012; Haris-
mendy et al., 2011; Maurano et al., 2012; Musunuru et al.,
2010). A CRE, such as a promoter or an enhancer, is a noncod-
ing DNA sequence in, near, or distal to a gene that contains
binding sites for regulatory factors and is required for proper
spatiotemporal expression of the gene. Long-distance en-
hancers are thought to interact physically with gene proximal
promoters and transcription start sites (TSSs) by forming loops
through regulatory proteins including cohesins and other re-
pressors and facilitators of transcription (Fanucchi et al.,
2013; Kagey et al., 2010). Because these chromosomal loop-
ings can bypass hundreds of kilobases on the linear genome,
risk loci positioned within CREs at a distance from the TSS
could affect the binding of these regulatory proteins and ulti-
mately lead to allele-specific differences in target gene ex-
pression and subsequent alterations in molecular pathways
implicated in disease.
In this study, we use functional annotations to categorize
GWAS SNPs and demonstrate that variants increasing risk for
SCZ are enriched for alleles that affect gene expression
(eSNPs) and lie within promoters or enhancers. The enrichment
shows tissue specificity and is greatest when functional
annotations derived from human cerebral cortex are used.
For ten out of 22 SCZ GWAS hits, we identify functional
variants positioned within promoters, enhancers, and other
regulatory sequences that are associated with expression of
13 genes. For the L-type calcium channel (CACNA1C), a
well-established SCZ risk locus, we map noncontiguous
physical interactions between enhancer regions and the
TSSs using human postmortem brain tissue and human
induced pluripotent stem cells (hiPSCs)-derived neurons. Over-
all, this study provides a functional link between SCZ noncod-
ing risk loci and physical interactions of noncontiguous DNA
elements associated with transcriptional regulation in the hu-
man brain.
RESULTS
Enrichment of Functional Annotation Categories in SCZ
We primarily used publically available data to generate functional
annotations. Brain eSNPs were generated by using genotype
and gene-expression profiles from eight data sets (Colantuoni
et al., 2011; Gibbs et al., 2010; Zhang et al., 2014;Table S1).
The brain CRE annotation map was generated based on
chromatin immunoprecipitation followed by high-throughput
sequencing (ChIP-seq) experiments of histone modifications
(Cheung et al., 2010; Maurano et al., 2012; Shulha et al., 2012,
2013; Zhu et al., 2013;Tables S2 and S3). We integrated data
from specific sets of histone methylation and acetylation mark-
ings and DNase I hypersensitive sites (DHSs) to define five types
of CREs: active promoter; active enhancer; poised promoter;
repressed enhancer; and open chromatin regions.
Genome-wide SNPs from a published SCZ GWAS data set
(Ripke et al., 2013) were classified into four different categories:
(1) eSNP: if they affect gene expression of specific transcripts; (2)
CRE: if they lie within a CRE region; (3) eSNP in a cis-regulatory
element (creSNP); or (4) functionally unannotated variants (FUV),
if they did not cluster to any of the above categories (Table S4).
Among SCZ nominally associated loci at p %10
3
(n = 42,253
SNPs), 37.3% were grouped into the eSNP category (n =
15,762; Table 1). Among this 37.3%, 4.9% were in active pro-
moters, 9.6% in active enhancers, 3.5% in DHSs, 1.0% in poised
promoters, and 1.5% in repressed enhancers. Relative enrich-
ments for the categories were calculated using an empirical
cumulative distribution of the GWAS p values after controlling
for genomic inflation as described previously (Schork et al.,
2013). Across all p value thresholds tested, the largest enrich-
ment of GWAS SNPs occurs in the following categories: eSNPs
and three types of CREs: active promoters, active enhancers,
and DHSs (Table 1;Figure 1). Despite having fewer SNPs,
enrichment is greater when the combined creSNP functional
category is analyzed for all types of CREs (CRE range: 1.58- to
7.08-fold; creSNP range: 4.03- to 29.51-fold). This indicates
that SCZ-associated variants are enriched for SNPs that
have stronger support for a functional role (creSNP). Higher
Table 1. SNP Enrichment for Different GWAS p Values
Functional Category
Number of SNPs
Number of SNPs (SNP Enrichment)
p<10
3
p<10
5
p<5310
8
CRE creSNP CRE creSNP CRE creSNP CRE creSNP
SCZ GWAS 9,815,700 42,253 4,337 692
eSNP 1,479,508 15,762 (3.68) 2,585 (8.07) 529 (14.13)
Active promoter
(H3K4me3 and [H3K9ac or H3K27ac])
209,349 51,728 1,363 (2.13) 778 (5.17) 172 (2.88) 142 (9.31) 18 (4.57) 17 (17.38)
Active enhancer
(H3K4me1 and [H3K9ac or H3K27ac])
419,981 95,701 2,858 (2.30) 1,518 (5.66) 353 (3.16) 290 (11.46) 59 (7.08) 54 (29.51)
DHS 276,468 46,770 1,365 (1.58) 558 (4.06) 158 (2.39) 118 (10.94) 26 (5.13) 23 (26.92)
Poised promoter
(H3K4me3 and H3K27me3)
81,260 13,743 357 (1.4) 155 (4.03) 27 (1.02) 25 (5.36) 3 (2.29) 3 (13.80)
Repressed enhancer
(H3K4me1 and H3K27me3)
165,117 25,547 623 (1.13) 241 (3.12) 46 (0.82) 34 (4.67) 5 (1.51) 5 (9.55)
The enrichment of each functional category is given in comparison to FUV.
2Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

enrichment of the creSNP in comparison to CRE categories
alone is found for the individual, nonintegrated CRE and creSNP
functional annotation categories (Figure S1;Table S5). Among
the individual, nonintegrated creSNP annotations, H3K4me1,
an individual histone mark of enhancers, in fetal and adult brain
tissue is the most-enriched category (Table S5).
We provide a single number quantification of enrichment by
calculating a categorical enrichment score (CES), which is a
conservative estimate of the variance attributable to nonnull
SNPs (Schork et al., 2013). The CES analysis indicates the
following: first, SNPs that cluster within CRE, eSNP, and creSNP
functional annotation categories show higher CES compared to
FUV (Figure 2). Second, the creSNP categories (scaled CES
creSNP range: 0.66–1) have higher CES than CREs (scaled
CES CRE range: 0.11–0.29). Third, certain creSNP categories
(active promoter, active enhancer, and DHS) were the most en-
riched as measured by the CES. The enrichment was significant
for active promoter and enhancer (for both CRE and creSNP),
eSNP, and DHS creSNP (all p %0.0001 by permutation). In the
individual nonintegrated functional categories, the H3K4me1
and H3K4me3 creSNP annotations in fetal brain tissue were
the most enriched (26-fold compared to FUV category; p %
0.0001 by permutation), as measured by the CES (Figure S2).
Differences in the extent of LD (estimated based on the sum r
2
)
and minor allele frequency (MAF) were observed between the
functional categories (Table S6). Because categories with higher
average MAF or larger total amount of LD could spuriously
appear enriched for SCZ association, we performed regression
analysis, which demonstrated that the effect of functional cate-
gories remains independently strong with an effect size rank
that mirrors enrichment, despite the significant correlation
among categories (Table S7). Furthermore, the enrichment was
significant for all functional categories compared to FUV after
removing SNPs with r
2
> 0.1 and those that were <100 kb from
a more strongly associated variant in the SCZ study (Table S6;
Figure S3).
Tissue Specificity of Functional Annotation Categories
for GWAS Enrichment
We then examined whether functional categories generated in
brain tissue can better inform SCZ SNPs (show higher CES)
compared to annotations derived from nonbrain tissues. We
Figure 1. Stratified Q-Q Plots for eSNP, CRE, and creSNP in Active Promoter, Active Enhancer, DHS, Poised Promoter, and Repressed
Enhancer Functional Annotation Categories
The numbers for each functional category (blue box: creSNP; green box: CRE) illustrate the estimated increase in terms of the proportion of p values expected
below a genome-wide significant p value (p < 5 310
8
; red dashed line) compared to the functionally unannotated variant (FUV) category. The estimated
enrichment for eSNPs is 14.1. For all functional categories, enrichment is greater when the creSNP functional category is analyzed relative to CREs. All summary
statistics were corrected for inflation by using the FUV inflation control. The major histocompatibility complex locus (chr6: 25–35 Mb) was excluded from the SCZ
data set.
Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors 3
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

used the following nonbrain eSNP-lymphoblastoid cell line (LCL)
(Xia et al., 2012), liver (Innocenti et al., 2011), peripheral blood
mononuclear cells (PBMCs) (Westra et al., 2013), skin, and adi-
pose tissue (Grundberg et al., 2012)—and CRE-skin, T-helper,
liver, and adipose tissue (Maurano et al., 2012; Zhu et al.,
2013)—functional categories to estimate CES for SCZ GWAS
as described above. In addition, we calculated CES using a pre-
viously published GWAS in rheumatoid arthritis (RA) (Stahl et al.,
2010). The PBMC eSNP and T-helper CRE functional categories
were selected as positive controls for RA because immunolog-
ical cells are implicated in its etiopathogenesis (Okada et al.,
2014; Trynka et al., 2013). The major histocompatibility complex
(MHC) locus (chr6: 25–35 Mb) was excluded from both GWAS
data sets. The brain eSNP and CRE functional category showed
the highest enrichment for SCZ (Figure 3A). In contrast, the
blood/T-helper functional category showed the highest enrich-
ment for RA. Within the brain and blood/T-helper related func-
tional categories, the active promoter, active enhancer, and
DHS show the highest enrichment for SCZ and RA SNPs,
respectively (Figure 3B).
Using Functional Annotations to Prioritize Risk Loci
in SCZ
The majority of SCZ genome-wide significant loci (index and
SNPs in LD with them) are noncoding (Ripke et al., 2013). Given
the enrichment of SCZ loci for eSNPs, we used the regulatory
trait concordance (RTC) approach (Grundberg et al., 2012;
Nica et al., 2010) to prioritize SNPs and genes within SCZ
genome-wide significant loci. RTC scores R0.9 indicate that
overlapping eSNP and GWAS signals likely tag the same variant.
The genome-wide significant SNPs in Ripke et al. were map-
ped to 22 hot spot intervals (Table 2). We detected overlapping
eSNP and GWAS signals at RTC R0.9 for 10 of 22 intervals,
four times the number expected by chance (2.2 expected in
the top 10% of scoring intervals under the uniform distribution;
Nica et al., 2010;p=2310
5
). The SCZ-related eSNPs are
associated with expression of 17 genes (three intervals had
RTC scores with eSNPs of R0.9 for more than one gene). Given
the enrichment of SCZ loci for creSNPs, we examined whether
any of the 17 SCZ-associated eSNPs (and tag SNPs within
500 kb and r
2
> 0.8) lie within the most-enriched CRE categories
(active promoter, active enhancer, and DHS). Thirteen eSNPs
out of the 17 are localized within such a CRE (Table 2;Figure 4).
The expression of five genes is associated with loci within
enhancers (C10orf32,CACNA1C,NGEF,RP11-490G2.2, and
SDCCAG8). Gene expression of AS3MT is influenced by an
eSNP that lies within the promoter region. The expression level
of the remaining genes (NT5C2,GATAD2A,HAPLN4,GNL3,
NEK4,SPCS1, and TYW5) is associated with multiple eSNPs
within both promoter and enhancer sequences.
Functional Annotations Identify Risk Variants in
CACNA1C that Lie within Putative Enhancers and Affect
Gene Expression
The stepwise approach described above (Table 2;Figure 4)
allows us to formulate a testable hypothesis for the mechanism
through which some variants might increase risk for SCZ. For
example, the CACNA1C index SNP (rs1006737) and eSNP
(rs758170) are in close proximity (16.2 kb) and have an RTC
score of 1. Furthermore, the risk allele is associated with
decreased CACNA1C gene expression (p = 1.88 310
5
at false
discovery rate [FDR] 0.7%). We identified four SNPs (rs2159100,
rs12315711, rs11062170, and rs4765905) that are in perfect
LD with rs758170 and rs1006737 and lie within two predicted
enhancers (spanning 1.4 kb and 1.85 kb), 185 kb downstream
from the gene’s TSS (Figures 5A and 5B). To identify whether
the predicted enhancer region might be capable of forming
promoter-enhancer loops, we mapped its physical interaction
with the CACNA1C TSS in human dorsolateral prefrontal
cortex (n = 6) and hiPSC-derived neurons by chromosome
conformation capture (3C) assay (Mitchell et al., 2014;Tables
S8 and S9). In addition, this approach allows us to dissect
the LD complexity of the region and identify variants with
additional support for a functional role. Of the 17 restriction
site regions tested, only one displayed an increased interac-
tion with the TSS in human postmortem tissue (primer no. 4 in
Figures 5A–5D). This enhancer region includes rs2159100
(MAF = 0.35; GWAS p value = 1.1 310
10
) and rs12315711
(MAF = 0.35; GWAS p value = 1.1 310
10
) and demonstrates
increased interaction frequency with the CACNA1C promoter
(F [16, 83] = 5.52; p = 8 310
8
). The rs2159100/rs12315711
3C interaction was confirmed in hiPSC-derived neurons (Fig-
ure 5D). In addition to being in an enhancer region, rs2159100
also colocalizes with a 600 bp DHS region. Thus, we examined
its effect on transcriptional activity in in vitro experiments.
Compared to the reference rs2159100 C allele, the risk T
variant is associated with decreased transcriptional activity in
human embryonic kidney 293 (HEK293) and Neuro-2a cells
Figure 2. Categorical Enrichment for the Combined Functional
Annotations as Measured by the CES
On the left side, we show the observed enrichment (red dashed lines) against
the null distribution (gray density plots). For each functional category, we
performed 10,000 permutations to calculate the null distribution of enrichment
for comparison to observed categorical enrichment. Functional categories
with empirical p values that survived Bonferroni multiple testing correction are
in bold (p corrected: 0.05/11 = 4.5 310
3
). The number in parentheses in-
dicates the number of SNPs per annotation category. On the right side, the bar
plot illustrates the scaled CES for each functional category. creSNPs are
illustrated in blue color, eSNPs in red, CREs in green, and FUV in black. The
CESs are scaled using the maximum value across functional categories. All
summary statistics were corrected for inflation by using the FUV inflation
control.
4Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

(42% [p < 0.0001] and 23% [p < 0.05] reduction in luciferase
activity, respectively; Figure 5E).
DISCUSSION
We have demonstrated that SCZ-associated loci are enriched
for certain functional annotation categories. As reported previ-
ously, we found enrichment with eSNPs (Richards et al., 2012)
and CRE annotations, highlighting active regulatory regions
(Trynka et al., 2013). Here, we demonstrate that integrative anal-
ysis of eSNPs with CRE epigenomic annotations identifies
greater enrichment of risk loci compared to eSNPs or CREs
alone. Given that eSNP- (Dimas et al., 2009; Fairfax et al.,
2012; Gibbs et al., 2010; Nica et al., 2011) and CRE-mediated
epigenetic regulation (Cheung et al., 2010; Heintzman et al.,
2009; Maurano et al., 2012) is often specific for tissue and
even cell type, our findings add to the growing evidence support-
ing the importance of studying the human brain tissue for func-
tional genomics analysis in neuropsychiatric illnesses.
The strongest SCZ-associated enrichment was observed in
fetal and adult brain creSNP annotations for enhancers. Previous
studies have established the important regulatory role of the en-
hancers on transcriptome organization during neurodevelop-
ment and adulthood (Andersson et al., 2014; Visel et al., 2013;
Wenger et al., 2013). Overall, these findings suggest that risk-
allele-specific alterations in enhancers could affect the proper
spatiotemporal organization of the transcriptome that, when
combined with other perturbations, leads to SCZ.
We have used a stepwise approach for defining functional
enrichment and, in so doing, were led to a mechanistic hypoth-
esis (of an interaction between disease signal, expression signal,
and an enhancer) about the formation of chromosome loops be-
tween the enhancer and promoter. We experimentally validated
these long-range interactions in human brain tissue and hiPSC-
derived neurons for a gene that has been strongly associated
with neuropsychiatric disorders. More specifically, CACNA1C,
a subunit of the L-type calcium channel, is one of the most widely
reproduced associations, first identified in bipolar disorder (Psy-
chiatric GWAS Consortium Bipolar Disorder Working Group,
2011; Ferreira et al., 2008; Sklar et al., 2008), but subsequently
also shown to be strongly associated with SCZ (Ripke et al.,
2013). The association signal is in the middle of an intron and
does not suggest any immediate functional possibilities. In addi-
tion, the associated region is large (154.7 kb) and contains mul-
tiple implicated SNPs due to local LD patterns (216 SNPs with
p<10
3
). We have now demonstrated in postmortem human
brain and hiPSC-derived neurons a specific interaction of a
narrow, 1.4 kb region (which is an enhancer) with the proximal
gene promoter by chromosome conformation capture. Further-
more, the risk variant is associated with reduced CACNA1C
gene expression and transcriptional activity in the eSNP and
in vitro experiments, respectively. Another recent study reported
that CACNA1C rs1006737 (or rs2159100) is associated with
decreased gene expression (Gershon et al., 2014), similar to
our findings, although this is not consistently observed (Bigos
et al., 2010). Since the initial report of CACNA1C association
with bipolar disorder (Ferreira et al., 2008), there has been
follow-up with studies that report effects on functional connec-
tivity in attention and emotion networks, cognitive performance,
and personality traits in SCZ and bipolar disorder (Bigos et al.,
2010; Erk et al., 2010; Hori et al., 2012; Paulus et al., 2014; Radua
et al., 2013; Roussos et al., 2011, 2013; Tesli et al., 2013).
Two out of the 17 genes identified through the RTC approach
are calcium channels subunit genes (CACNA1C and CACNB2).
We note that calcium channel subunits have been previously
implicated in GWAS of bipolar disorder (Ferreira et al., 2008;
Lee et al., 2011; Sklar et al., 2008; Psychiatric GWAS Consortium
Bipolar Disorder Working Group, 2011), SCZ (Ripke et al., 2013),
and cross-disorder analyses (Cross-Disorder Group of the Psy-
chiatric Genomics Consortium, 2013). In addition, an enrichment
of rare disruptive variants in calcium channel subunits was re-
ported in a recent exome-sequencing study (Purcell et al.,
Figure 3. Categorical Enrichment in the SCZ and RA GWAS Data Sets for eSNPs and CREs
For each eSNP-CRE combination, the (A) average value of the CES across all functional categories (active promoter, active enhancer, DHS, poised promoter, and
repressed enhancer) or (B) individual value was calculated. For each GWAS data set, the CESs were scaled using the maximum value across functional cate-
gories. The brain- and blood/T-helper-related eSNP and CRE functional category showed the highest enrichment for SCZ (blue) and RA (red) SNPs, respectively.
All summary statistics were corrected for inflation by using the FUV inflation control. *p < 0.05 and **p < 0.01 by nonparametric Mann-Whitney among the most-
enriched category and the rest of functional categories for each GWAS data set. AE, active enhancer; AP, active promoter; PP, poised promoter; RE, repressed
enhancer.
Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors 5
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

Table 2. Annotation of the 22 Genome-wide Significant Loci Using the Functional eSNP and CRE Data
SCZ GWAS Recombination Interval
eSNP
b
Distance (kb)
c
RTC Analysis
Chromosomal Region Index SNP p Size (kb) Genes
a
r
2
Gene RTC Beta (SE)
d
creSNP
e
CRE
Chr. 6: 31,596,138–
32,813,768
rs114002140 9.14 310
14
1,905.5 263 (127) NA – – – – – –
Chr. 10: 104,487,871–
105,245,420
rs7085104 3.68 310
13
4,807.9 135 (85) rs4919690
f
12.4 0.64 AS3MT 1 0.72 (0.07) 1 AP/DHS
rs4919690
f
12.4 0.64 C10orf32 1 0.51 (0.07) 1 AE/DHS
rs56946876
f
24.7 0.68 NT5C2 0.98 0.90 (0.04) 14 AP/AE/DHS
rs619824
f
47.6 0.62 WBP1L 0.99 0.64 (0.07) – –
Chr. 7: 1,827,717–
2,346,115
rs6461049 5.93 310
13
3,196.4 66 (39) rs12154473
f
35.3 0.85 SNX8 0.97 0.34 (0.09) – –
Chr. 1: 98,141,112–
98,664,991
rs1198588 1.72 310
12
775.5 24 (2) rs1198572
f
55.7 0.87 RP11-
490G2.2
0.98 0.40 (0.08) 1 AE/DHS
Chr. 12: 2,285,731–
2,440,464
rs1006737 5.22 310
12
1,339.0 61 (17) rs758170
f
16.2 0.97 CACNA1C 1 0.39 (0.09) 4 AE/DHS
Chr. 10: 18,601,928–
18,934,390
rs17691888 1.27 310
10
882.1 36 (4) rs10828653
f
38.2 0.59 CACNB2 1 0.34 (0.08) – –
Chr. 8: 143,297,312–
143,410,423
rs4129585 2.19 310
10
538.9 68 (16) rs11988625 7.4 0.52 LYPD2 0.89 0.33 (0.09) NA NA
Chr. 1: 73,275,828–
74,099,273
rs10789369 3.64 310
10
1,814.3 33 (3) rs10890066 346.9 0.002 CRYZ 0.48 0.30 (0.08) NA NA
Chr. 11: 130,706,918–
130,894,976
rs7940866 1.83 310
9
240.4 34 (7) rs10791107 28.9 0.78 APLP2 0.88 0.36 (0.09) NA NA
Chr. 5: 151,888,959–
152,835,304
rs17504622 2.65 310
9
1,242.4 34 (9) NA – – – – – –
Chr. 19: 19,354,937–
19,744,079
rs2905424 3.44 310
9
7,682.3 321 (160) rs7254230
f
39.1 0.91 GATAD2A 1 0.38 (0.08) 14 AP/AE/DHS
rs2074295
f
104.0 0.45 GMIP 0.99 0.32 (0.08) – –
rs12460764
f
41.5 0.91 HAPLN4 1 0.34 (0.08) 14 AP/AE/DHS
Chr. 2: 37,422,072–
37,592,628
rs2373000
g
6.78 310
9
666.1 32 (13) rs12621276 293.5 0.06 EIF2AK2 0.89 0.40 (0.09) NA NA
Chr. 5: 101,581,848–
101,870,822
rs6878284
g
9.03 310
9
3,643.4 42 (8) NA – – – – – –
Chr. 3: 52,215,002–
53,175,017
rs4687552 1.16 310
8
7,777.1 294 (142) rs12486554
f
95.9 0.75 GNL3 0.99 0.40 (0.08) 15 AP/AE/DHS
rs2268023
f
19.1 0.78 NEK4 0.95 0.28 (0.07) 13 AP/AE/DHS
rs13071584
f
33.9 0.74 SPCS1 0.99 0.34 (0.08) 14 AP/AE/DHS
(Continued on next page)
6Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

Table 2. Continued
SCZ GWAS Recombination Interval
eSNP
b
Distance (kb)
c
RTC Analysis
Chromosomal Region Index SNP p Size (kb) Genes
a
r
2
Gene RTC Beta (SE)
d
creSNP
e
CRE
Chr. 2: 145,139,727–
145,214,607
rs12991836 1.19 310
8
1,164.0 29 (5) rs72858496 68.4 0.01 GTDC1 0.8 0.38 (0.08) NA NA
Chr. 2: 200,628,118–
201,293,421
rs2949006 1.21 310
8
1,916.3 61 (18) rs35220450
f
65.3 0.83 TYW5 0.98 0.52 (0.07) 3 AP/AE/DHS
Chr. 18: 52,722,378–
52,827,668
rs4801131 1.22 310
8
1,047.2 33 (10) rs8084537 121.7 0.002 TCF4 0.15 0.33 (0.08) NA NA
Chr. 2: 233,550,961–
233,808,241
rs778371 1.51 310
8
1,945.1 105 (42) rs778371 0.0 – NGEF 1 0.56 (0.07) 7 AE
Chr. 1: 243,593,066–
244,025,999
rs14403 1.80 310
8
1,614.2 51 (11) rs3006916
f
24.0 0.64 SDCCAG8 0.98 0.42 (0.09) 3 AE/DHS
Chr. 12: 123,447,928–
123,913,433
rs11532322 2.28 310
8
2,236.6 101 (50) NA – – – – – –
Chr. 1: 243,418,063–
243,627,135
rs1538774 2.53 310
8
1,614.2 51 (11) rs3006916 95.0 0.02 SDCCAG8 0.57 0.42 (0.09) NA NA
Chr. 8: 89,188,454–
89,761,163
rs11995572 3.33 310
8
1,550.2 24 (7) NA – – – – – –
Chr. 5: 60,484,179–
60,843,706
rs171748 3.78 310
8
2,761.2 48 (14) rs295571 72.1 0.20 PDE4D 0.87 0.31 (0.08) NA NA
Chr. 5: 152,505,453–
152,707,306
rs2910032 4.12 310
8
1,242.4 34 (9) rs2118792 30.2 0.07 FAM114A2 0.88 0.37 (0.08) NA NA
AE, active enhancer; AP, active promoter; DHS, DNase I hypersensitive site; RTC, regulatory trait concordance.
a
Number of genes (based on the Gencode v16 annotations) that lie within 1 Mb upstream or downstream from recombination intervals. In parentheses are the numbers of genes that were affected
by eSNPs and included in the RTC analysis for each recombination interval.
b
eSNP with the highest RTC score for each SCZ GWAS chromosomal region. NA indicates that the GWAS SNP was excluded from the eSNP analysis due to MAF < 5% (rs17504622) or increased
missingness (>10%) per marker after imputation (rs6878284, rs114002140, rs11532322, and rs11995572).
c
Distance among the eSNP and index SCZ GWAS SNP.
d
Standardized beta coefficient and SE for the effect of minor allele on gene expression.
e
Number of creSNPs that are in strong LD (within 500 kb and with r
2
> 0.8) with the eSNP.
f
eSNPs with RTC R0.9. For GWAS regions with no eSNP at RTC R0.9, we present the eSNP with the highest RTC. For those SNP, no creSNP or CRE data are presented.
g
This region was not genome-wide significant in the recent PGC2 GWAS analysis (Schizophrenia Working Group of the Psychiatric Genomics Consortium, 2014).
Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors 7
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

2014). CACNA1C codes for Ca
v
1.2, the most abundant neuronal
L-type calcium channel (Obermair et al., 2004). The a
1c
subunit
(CACNA1C) forms the transmembrane pore and directly inter-
acts with the intracellular b
2
subunit (CACNB2). The cytosolic
b
2
subunit has a major role in stabilizing the a
1
subunit conforma-
tion and delivering it to the cell membrane by its ability to mask
an ER retention signal in the a
1
subunit (Bichet et al., 2000).
Calcium-mediated signaling has an important role on neuronal
differentiation by regulating axonal growth and guidance,
and this process is also controlled by glutamatergic signaling
Figure 4. Functional Genomic Analysis for the SCZ Genome-wide Significant Loci
Layer 1 shows the 24 genome-wide significant loci. Green lines illustrate loci with log10 p value %10, and red lines show loci with log10 p value > 10. Layer 2
(eSNP) illustrates which of the 24 significant loci had eSNP with RTC R0.9. Layers 3–5 show whether eSNPs (and tag SNPs with r
2
> 0.8 within 500 kb) lie within
active promoter (layer 3; promoter), active enhancer (layer 4; enhancer), or DNase I hypersensitive site (layer 5; DHS). Genes affected by functional SNPs are
illustrated outside the circo. In black fonts are genes affected by eSNP. In red fonts are genes affected by creSNPs (within active promoter, active enhancer,
or DHS).
8Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

(Rosenberg and Spitzer, 2011). It is possible that altered tuning in
calcium-mediated signaling triggered by Ca
v
1.2 and glutamater-
gic neurotransmission (Fromer et al., 2014; Purcell et al., 2014)
could lead to alterations in the rate of axon outgrowth and path-
finding, resulting in inefficient neuronal wiring in SCZ.
Whereas our approach can identify functional categories with
higher enrichment compared to FUV categories, we still observe
a deviation from the null for the FUV category, indicating multiple
SCZ-associated loci that were not captured through our current
functional annotation categories. Clearly, current databases do
not yet capture all types of functional variants, including sites
of DNA methylation and hydroxymethylation (Lister et al.,
2013), as well as additional CREs such as insulators (Herold
et al., 2012). Furthermore, there is relatively low genomic resolu-
tion of current functional categories and many additional alterna-
tive putative mechanisms, such as transcriptional regulation
through small and long noncoding RNAs and alternative splicing,
likely mediate the effect of some noncoding risk alleles.
In conclusion, these results suggest a tissue-specific regula-
tory role for many SCZ-associated common loci. While this
paper was under review, a mega-analyses by the Psychiatric
Genomic Consortium (PGC) in SCZ on over 80,000 cases and
controls was published (Schizophrenia Working Group of the
Psychiatric Genomics Consortium, 2014). In the new PGC
GWAS, 22 out of 24 loci remain genome-wide significant. In
addition, 19 out of the 24 SNPs presented in Table 2 were in
LD (r
2
R0.3) with a genome-wide significant PGC index SNP.
Our analysis provides a framework for future integrative analysis
of additional data sets to generate testable hypotheses and
derive mechanistic insights for SCZ-associated variants.
EXPERIMENTAL PROCEDURES
A brief description of key methods and sample description are provided below,
whereas complete details are found in the Supplemental Experimental
Procedures.
GWAS Data Sets
A large published SCZ GWAS data set (Ripke et al., 2013) in the form of
summary statistic p values was obtained from public access website (http://
www.med.unc.edu/pgc/). A previously published GWAS data set in rheuma-
toid arthritis (Stahl et al., 2010) was obtained through collaboration with
investigators in the form of summary statistic p values. For all the analyses
Figure 5. A Physical Interaction between the CACNA1C Promoter and an Enhancer Region Was Confirmed by 3C
(A) Part of the genomic region of CACNA1C (chr12: 2,303,497–2,419,832) is displayed. The index SNP (red line; rs1006737 ), eSNP (orange line; rs758170), and tag
SNPs (blue line; r
2
> 0.8 within 500 kb) that lie within CREs (enhancer and DHS) are illustrated. The index SNP and SNPs in LD with them are associated with lower
CACNA1C gene expression. 3C-PCR primers were designed at the CACNA1C TSSs and multiple regions (primers nos. 1–17). A 3C physical interaction betwee n
the CACNA1C TSS and primer no. 4 was found in 3C libraries made from postmortem brain tissue (n = 6; F [16, 83] = 5.52; p = 8 310
8
).
(B) More detailed view of the associated region (chr12: 2,344,353–2,362,387). The primer no. 4 includes the rs2159100 creSNP (GWAS p value = 1.1 310
10
),
which lies within an active enhancer (green box) and DHS (orange box).
(C) 3C-qPCR shows increased interaction for primer no. 4 in libraries made from postmortem brain tissue (n = 6; F [2, 15] = 4.54; p = 0.029).
(D) Gel images are shown for primer no. 4 for 3C interactions using prefrontal cortex libraries in controls and SCZ- and hiPSC-derived neurons. The red arrow
shows the 3C interaction band. All 3C PCR products were sequence verified, and the interactions were not present in the no ligase (L) and water (W) controls.
(E) The rs2159100 T risk allele (position 257 in the construct: 257T) affects the relative luciferase activity in HEK293 and Neuro-2a cells compared to the C
allele (257C).
Data show the mean and SEM. *p < 0.05 and ****p < 0.0001 by unpaired t test.
Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors 9
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

presented here, the MHC locus (chr6: 25–35 Mb) was excluded from both
GWAS data sets.
eSNP Data Sets
Brain eSNPs were generated using the gene expression and genotyping data
of Caucasian samples, included in the Braincloud (Colantuoni et al., 2011;
Gene Expression Omnibus [GEO] accession number: GSE30272), NIA/NIH
(Gibbs et al., 2010; GEO accession number: GSE15745), and Harvard Brain
Tissue Resource Center (Zhang et al., 2014; GEO accession number:
GSE44772) data sets (Table S1). The following nonbrain eSNP data sets
were downloaded from public access websites: LCL (Xia et al., 2012;http://
www.bios.unc.edu/research/genomic_software/seeQTL/), liver (Innocenti
et al., 2011;http://www.scandb.org/), PBMCs (Westra et al., 2013;http://
genenetwork.nl/bloodeqtlbrowser), skin (Grundberg et al., 2012), and adipose
tissue (Grundberg et al., 2012;http://www.muther.ac.uk/Data.html).
cis-Regulatory Element Annotations
Multiple CRE annotations were used in the current study (Tables S2 and S3).
ChIP-seq and DHS data generated as part of the ENCODE (Maurano et al.,
2012) and REMC (Zhu et al., 2013) projects for human brain/neuron (Table
S2), T-helper cells, liver, skin, and adipose tissue were downloaded from the
National Center for Biotechnology Information repository (http://www.ncbi.
nlm.nih.gov/geo/roadmap/epigenomics/). Additional data for the dorsolateral
prefrontal cortex after fluorescence-activated cell sorting were generated as
described previously (Cheung et al., 2010; Shulha et al., 2012, 2013;Table S3).
Definition of Functional Data Sets
All SNP coordinates described here are relative to UCSC hg19. The functional
data sets used in the current study were divided into three groups: eSNP, CRE
and creSNP (eSNP in a cis-regulatory element).
(1) eSNP: the brain eSNP data set was generated by including all signifi-
cant cis eSNPs derived from each eSNP analysis. For the nonbrain
eSNPs (LCL, liver, skin, PBMCs, and adipose tissue), we used the list
of cis eSNPs generated as described previously (Grundberg et al.,
2012; Innocenti et al., 2011; Westra et al., 2013; Xia et al., 2012)at
FDR 10%.
(2) CRE: the ChIP-seq and DHS significant peaks were clustered into sub-
groups based on assay and origin of tissue (Figure S4). We integrated
multiple CRE subgroup annotations for generating functional annota-
tions defining active promoters (overlap of H3K4me3 with H3K9ac or
H3K27ac), poised promoters (overlap of H3K4me3 with H3K27me3),
active enhancers (overlap of H3K4me3 with H3K9ac or H3K27ac),
repressed enhancers (overlap of H3K4me1 with H3K27me3), and
open chromatin (DHS).
(3) creSNP: the creSNP functiona ldata set was defined as the eSNPs that
lie within different CRE subcategories.
GWAS Positional Annotation
We used a mixed approach for assigning the GWAS SNPs into functional cat-
egories. For the eSNP functional category, we leveraged the eSNP data set in
the densely mapped 1000G to identify the GWAS studied SNP that was
tagged, as a result of LD. For generating the CRE or creSNP functional cate-
gories, we used a positional approach (ignoring the annotation categories of
SNPs in LD with the tag SNP). This mixed model allows us to capture all
possible SNPs that affect gene expression (tag or SNPs in LD), followed by
positional selection of SNPs that lie within putative regulatory DNA regions.
GWAS SNP that did not fit in any functional category was assigned as the
FUV category. The Table S4 describes the count of SCZ for each functional
brain category.
Quantification of Enrichment
Stratified Q-Q plots were generated for assessment of the similarity or differ-
ences between the empirical cumulative distribution function of the functional
and FUV data sets. In the stratified Q-Q plots, the enrichment of SCZ SNPs for
a specific functional category is observed as a horizontal deflection from the
FUV category. The quantification of enrichment for each functional category
was done using the CES (mean [z
2
1]), as described previously (Schork
et al., 2013). The CES provides a summary score of category-specific enrich-
ment where the mean is taken over all SNP Zscores in the given category. For
each functional category, the statistical significance of CES was evaluated by
permutation on a combined 10,000 randomized set of CREs and eSNPs.
Regulatory Trait Concordance Score
The likelihood of a shared functional effect between a SCZ genome-wide sig-
nificant SNP and an eSNP was assessed by the RTC approach (Grundberg
et al., 2012; Nica et al., 2010). RTC score ranges from 0 to 1, with values R0.9
indicating the GWAS signal and eSNP tag the same underlying signal, as
demonstrated previously (Grundberg et al., 2012; Nica et al., 2010).
Chromosome Conformation Capture
Postmortem prefrontal cortex brain tissue for cases with SCZ and controls was
obtained from the University of Maryland and pair matched for age, sex, post-
mortem interval, and pH (n = 3/group; Table S8). Chromosome conformation
capture (3C) was performed as described in a recently published protocol
applicable to postmortem brain (Mitchell et al., 2014). Physical looping interac-
tions were quantified with PCR. Primers were designed less than 120 bp from
the HindIII or NcoI restriction site (Table S9). The PCR products were resolved
on a 2% agarose gel, and the level of interaction between two primers was
measured semiquantitatively using band intensities normalized with the back-
ground (raw 3C interaction) with ImageJ (Schneider et al., 2012). For each
library (HindIII and NcoI) in the human postmortem brain tissue studies, we
transformed the raw 3C interaction to Zscores, followed by scaling (0 to 1;
scaled 3C interaction). All 3C PCR products were sequence verified, and the
interactions were not present in the no ligase and water controls. For primers
no. 2, no. 4, and no. 5, physical looping interactions were further quantified
with quantitative PCR (qPCR) using an ABI Prism 7900 (Applied Biosystems).
The reactions were run in triplicate for each sample, and DNA PCR product
was measured through SYBR Green I (Life Technologies).
Human Induced Pluripotent Stem Cells Differentiation to Neurons
hiPSCs were derived from fibroblasts of a control sample (GM03651) as
described previously (Brennand et al., 2011). hiPSC-derived neurons were
differentiated for 6 weeks in neural differentiation media. The majority of fore-
brain hiPSC neurons are VGLUT1-positive and so are presumably glutamater-
gic, although approximately 30% of neurons are GAD67-positive (GABAergic ;
Brennand et al., 2011).
Transient Transfection and Luciferase Assays
We constructed luciferase reporter plasmids by cloning the regulatory
sequence containing rs2159100 into the pGL4.24 vector (Promega) upstream
of the minP. HEK293 cells or Neuro-2a cells (40%–60% confluent) were trans-
fected with each construct (500 ng) and the Renilla luciferase expression vec-
tor pRL-TK (200 ng; Promega). The luciferase activity in the cell lysates was
determined using the Dual Luciferase Reporter System (Promega). Firefly lucif-
erase activities were normalized to that of Renilla luciferase, and expression
relative to the activity of the rs2159100 C allele was noted.
ACCESSION NUMBERS
The GEO accession number for the H3K4me3 ChIP-seq data reported in this
paper (Table S3) is GSE62391.
SUPPLEMENTAL INFORMATION
Supplemental Information includes Supplemental Experimental Procedures,
five figures, and nine tables and can be found with this article online at
http://dx.doi.org/10.1016/j.celrep.2014.10.015.
AUTHOR CONTRIBUTIONS
P.R., E.E.S., S.A., and P.S. designed and supervised the research. P.R.,
E.A.S., D.M.R., A.C., M.F., and S.M.P. performed the statistical analysis.
10 Cell Reports 9, 1–13, November 20, 2014 ª2014 The Authors
Please cite this article in press as: Roussos et al., A Role for Noncoding Variation in Schizophrenia, Cell Reports (2014), http://dx.doi.org/10.1016/
j.celrep.2014.10.015

A.C.M., J.F.F., V.M.P., J.T., and S.A. performed the chromatin conforma-
tion capture experiments. G.V., A.G., and N.K.R. performed the luciferase
assay. K.B. generated the hiPSCs. Y.O., K.A.S., J.W., L.P., L.K., P.K.G.,
R.M.P., and S.R. provided the GWAS in rheumatoid arthritis. P.R., S.A., and
P.S. prepared the manuscript. P.R. and A.C.M. contributed equally to this
work.
ACKNOWLEDGMENTS
We thank Iris Cheung and Yin Guo for ChIP-seq assays on sorted brain nuclei.
We thank all members of the Rheumatoid Arthritis Consortium for providing
access to the GWAS data. Members of Rheumatoid Arthritis Consortium are
Steve Eyre, John Bowes, Dorothe
´e Diogo, Annette Lee, Anne Barton, Paul
Martin, Alexandra Zhernakova, E.A.S., Sebastien Viatte, Kate McAllister,
Christopher I. Amos, L.P., Rene E. M. Toes, Tom W. J. Huizinga, Cisca Wij-
menga, Gosia Trynka, Lude Franke, Harm-Jan Westra, Lars Alfredsson, Xinli
Hu, Cynthia Sandor, Paul I. W. de Bakker, Sonia Davila, Chiea Chuen Khor,
Khai Koon Heng, Robert Andrews, Sarah Edkins, Sarah E. Hunt, Cordelia
Langford, Deborah Symmons, Biologics in Rheumatoid Arthritis Genetics
and Genomics Study Syndicate, Wellcome Trust Case Control Consortium,
Pat Concannon, Suna Onengut-Gumuscu, Stephen S. Rich, Panos Deloukas,
Miguel A. Gonzalez-Gay, Luis Rodriguez-Rodriguez, Lisbeth A
¨rlsetig, Javier
Martin, Solbritt Rantapa
¨a
¨-Dahlqvist, R.M.P., S.R., L.K., P.K.G., J.W., the Bio-
logics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate
(BRAGGSS), and the Wellcome Trust Case Control Consortium (WTCCC).
We thank Dr. Ron Zielke and staff from the Brain and Tissue Bank for Develop-
mental Disorders, and Dr. Andree Lessard from the Maryland Psychiatric
Research Center, University of Maryland, for providing postmortem brain tis-
sue. We acknowledge funding support from NIH/National Institute of Mental
Health (NIMH) grant R01MH095034 (to P.S.), NIMH grant R01MH097276 (to
P.S. and E.E.S.), NIMH grant U01MH103392 (to. S.A. and P.S.), NIMH grant
P50 MH096890 (to S.A.), National Institute of Neurological Disorders and
Stroke (NINDS) grant R21 NS076958 (to S.A.), NINDS grant R01 NS047229
(to N.K.R.), National Institute on Aging (NIA) grant R37 AG017926 (to N.K.R.),
NIA grant P50 AG005138 (to N.K.R. and A.G.), Veterans Affairs Merit grant
BX002395 (to P.R.), the Brain Behavior Research Foundation (to P.R.,
A.C.M., S.A., E.A.S., and K.B.), the American Psychiatric Associatio n-Merck &
Co. Early Academic Career Research Award (to P.R.), NIMH grant R01
MH101454 (to K.B.), the New York Stem Cell Foundation (to K.B.), Alzheimer’s
Association grant IIRG-11-205149 (to A.G.), the Friedman Brain Institute at
Icahn School of Medicine at Mount Sinai, and the Icahn Institute for Genomics
and Multiscale Biology at Icahn School of Medicine at Mount Sinai. This work
was supported in part through the computational resources and staff expertise
provided by the Department of Scientific Computing at the Icahn School of
Medicine at Mount Sinai. The funders had no role in study design, execution,
analysis, or manuscript preparation.
Received: May 24, 2014
Revised: July 31, 2014
Accepted: October 3, 2014
Published: November 6, 2014
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