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The GTEx Consortium atlas of genetic regulatory effects across human tissues
The Genotype Tissue Expression Consortium
Abstract
The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects
on the transcriptome across human tissues, and to link these regulatory mechanisms to trait and
disease associations. Here, we present analyses of the v8 data, based on 17,382 RNA-sequencing
samples from 54 tissues of 948 post-mortem donors. We comprehensively characterize genetic
associations for gene expression and splicing in cis and trans, showing that regulatory associations
are found for almost all genes, and describe the underlying molecular mechanisms and their
contribution to allelic heterogeneity and pleiotropy of complex traits. Leveraging the large
diversity of tissues, we provide insights into the tissue-specificity of genetic effects, and show that
cell type composition is a key factor in understanding gene regulatory mechanisms in human
tissues.
Introduction
A pressing need in human genetics remains the characterization and interpretation of the
function of the millions of genetic variants across the human genome. This is essential for
identifying the molecular mechanisms of genetic risk for complex traits and diseases, mainly
driven by non-coding loci with largely unknown regulatory functions. To address this challenge,
several projects have built comprehensive annotations of genome function across tissues and cell
types (1, 2), and mapped the effects of regulatory variation across large numbers of individuals,
primarily from whole blood and blood cell types (3-5). The Genotype-Tissue Expression (GTEx)
project provides an essential intersection where variant function can be studied across a wide range
of both tissues and individuals.
The GTEx project was launched in 2010 with the aim of building a catalog of genetic
effects on gene expression across a large number of human tissues in order to elucidate the
molecular mechanisms of genetic associations with complex diseases and traits, and improve our
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understanding of regulatory genetic variation (6). The project set out to collect biospecimens from
~50 tissues from up to ~1000 postmortem donors, and to create standards and protocols for
optimizing postmortem tissue collection and donor recruitment (7, 8), biospecimen processing (7),
and data sharing (www.gtexportal.com).
Following the earlier publication of the GTEx pilot (9) and mid-stage results (10), we
present a final analysis from the GTEx Consortium based on the v8 data release. We provide the
largest catalog to date of genetic regulatory variants affecting gene expression and splicing in cis
and trans across 49 tissues, and describe patterns and mechanisms of tissue- and cell type
specificity of genetic regulatory effects. Through integration of GTEx data with genome-wide
association studies (GWAS), we characterize mechanisms of how genetic effects on the
transcriptome mediate complex trait associations.
Figure 1. Sample and data types in the GTEx v8 study. (A) Illustration of the 54 tissue types (including 11
distinct brain regions and 2 cell lines), with sample numbers from genotyped donors in parentheses and color coding
indicated in the adjacent circles. Tissues with ≥70 samples were included in QTL analyses. (B) Illustration of the
core data types used throughout the study. Gene expression and splicing were quantified from bulk RNA-seq of
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heterogenous tissue samples, and local and distal genetic effects (cis-QTLs and trans-QTLs, respectively) were
quantified across individuals for each tissue.
QTL discovery
The GTEx v8 data set consists of 948 donors and 17,382 samples from 52 tissues and two
cell lines, with 838 donors and 15,253 samples having both RNA sequence (RNA-seq) and
genotype data from whole genome sequencing (WGS) (figs. 1a, S1–2). The 838 donors were
85.3% European American, 12.3% African American, and 1.4% Asian American. Of the 54
tissues, 49 had samples from at least 70 individuals and were used for analyses of quantitative trait
loci (QTL) (15,201 samples total). WGS was performed for each donor to a median depth of 32x,
resulting in the detection of a total of 43,066,422 single nucleotide polymorphisms (SNPs) after
QC and phasing (10,008,325 with MAF ≥ 0.01) and 3,459,870 small indels (762,535 with MAF ≥
0.01) (fig. S3, table S1, (11)). The mRNA of each of the tissue samples was sequenced to a median
depth of 82.6 million reads, and alignment, quantification and quality control were performed as
described in (11) (figs. S4–5).
The resulting data provide the broadest survey of individual- and tissue- specific gene
expression to date, enabling a comprehensive view of the impact of genetic variation on gene
expression and splicing (fig. 1b). Across all tissues, we discovered cis-eQTLs (5% FDR, per tissue
(11)) for 18,262 protein coding and 5,006 lincRNA genes (23,268 total cis-eGenes, corresponding
to 94.7% of all protein coding and 67.3% of all detected lincRNA genes detected in at least one
tissue), with a total of 4,278,636 genetic variants (43% of all variants with MAF ≥ 0.01) that were
significant in at least one tissue (cis-eVariants) (figs. 2a, S6, table S2). Cis-eQTLs for all long non-
coding RNAs (lncRNAs) are characterized in a companion analysis (12). The genes lacking a cis-
eQTL were enriched for those lacking expression in the tissues analyzed by GTEx, including genes
involved in early development (fig. S7). While most of the discovered cis-eQTLs had small effect
sizes measured as allelic fold change (aFC), across tissues an average of 22% of cis-eQTLs had an
over 2-fold effect on gene expression (fig. S10). We mapped splicing QTLs in cis with intron
excision ratios from LeafCutter (11, 13), and discovered 12,828 (66.5%) protein coding and 1,600
(21.5%) lincRNA genes (14,424 total) with a cis-sQTL (5% FDR, per tissue) in at least one tissue
(cis-sVariants) (fig. 2a, table S2). As expected (10), cis-QTL discovery was highly correlated with
the sample size for each tissue (Spearman’s rho = 0.95 for cis-eQTLs, 0.92 for cis-sQTLs).
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Previous studies have shown widespread allelic heterogeneity of gene expression in cis,
i.e., multiple independent causal eQTLs per gene (4, 14, 15). We used two approaches to
characterize this: 1) stepwise regression to identify conditionally independent cis-eQTLs, where
the threshold for significance was defined by the single cis-eQTL mapping (10), and 2) a Bayesian
approach where the posterior probability of linked variants was used to control the local FDR (11,
16). Both methods showed concordant results of widespread allelic heterogeneity, with up to 50%
of eGenes having more than one independent cis-eQTL in the tissues with the largest sample sizes
(figs. 2b, S8). Our analysis captured a lower rate of allelic heterogeneity for cis-sQTLs, which can
be a result of both underlying biology and lower power in cis-sQTL mapping (fig. S8). These
results highlight continued gains in cis-eQTL mapping with increasing sample sizes even when
the discovery of new eGenes in specific tissues starts to saturate.
Trans-eQTL mapping yielded 143 trans-eGenes (121 protein coding and 22 lincRNA at
5% FDR assessed at the gene level, separately for each gene type), after controlling for false
positives due to read misalignment (11, 17) (table S13). The number of trans-eGenes discovered
per tissue is correlated with sample size (Spearman’s rho = 0.68), and to the number of cis-eQTLs
(rho = 0.77), with outlier tissues such as testis contributing disproportionately to both cis and trans
(fig. 2c). We identified a total of 49 trans-eGenes in testis, with 47 found in no other tissue even
at FDR 50%. Over two-fold effect sizes on trans-eGene expression were observed for 19% of
trans-eQTLs (fig. S10). Trans-sQTLs mapping yielded 29 trans-sGenes (5% FDR, per tissue),
including a replication of a previously described trans-sQTL (3) and visual support of the
association pattern in several loci (11) (fig. S9, table S14). These results suggest that while trans-
sQTL mapping is challenging, we can discover robust genetic effects on splicing in trans.
We produced allelic expression (AE) data using two complementary approaches (11). In
addition to the conventional AE data for each heterozygous genotype, we produced AE data by
haplotypes, integrating data from multiple heterozygous sites in the same gene, yielding 153
million gene-level measurements (≥8 reads) across all samples (18). Allelic expression reflects
differential regulation of the two haplotypes in individuals that are heterozygous for a regulatory
variant in cis; indeed, cis-eQTL effect size is strongly correlated with allelic expression (median
rho = 0.82) (10). We hypothesized that cis-sQTLs could also partially contribute to allelic
imbalance even if only for parts of transcripts. However, there is drastically less signal of increased
allelic imbalance among individuals heterozygous for cis-sQTLs (median Spearman’s rho = -0.05)
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(fig. S11). This indicates that allelic expression data captures primarily cis-eQTL effects and
genetic splicing variation in cis is not strongly reflected in gene-level AE data.
Figure 2. QTL discovery. (A) The number of genes with a cis-eQTL (eGenes) or cis-sQTL (sGenes) per tissue, as a
function of sample size. See Fig. 1A for the legend of tissue colors. (B) Allelic heterogeneity of cis-eQTLs depicted
as proportion of eGenes with ≥1 independent cis-eQTLs (blue stacked bars; left y-axis) and as a mean number of cis-
eQTLs per gene (red dots; right y-axis). The tissues are ordered by sample size. (C) The number of genes with a trans-
eQTL as a function of the number of cis-eGenes. (D) Sex-biased cis-eQTL for AURKA in skeletal muscle, where
rs2273535-T is associated with increased AURKA expression in males (p = 9.02x10-27) but not in females (p = 0.75).
(E) Population-biased cis-eQTL for SLC44A5 in esophagus mucosa (allelic fold change = -2.85 and -4.82 in African
Americans (AA) and European Americans (EA), respectively; permutation p-value = 1.2x10-3).
Genetic regulatory effects across populations and sexes
Variability in human traits and diseases between sexes and population groups is likely to
partially derive from differences in genetic effects (19-21). To study this, we analyzed variable
cis-eQTL effects between males and females, as well as between individuals of European and
African ancestry. Since external replication data sets are sparse, we use a novel allelic expression
approach for validation with an orthogonal data type from the same samples (18): allelic imbalance
in individuals heterozygous for the cis-eQTL allows individual-level quantification of the cis-
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eQTL effect size (22), and can be correlated with the interaction terms used in cis-eQTL analysis
to validate modifier effects of the cis-eQTL association.
To characterize sex-differentiated genetic effects on gene expression in GTEx tissues, we
mapped sex-biased cis-eQTLs (sb-eQTLs). Analyzing the set of all conditionally independent cis-
eQTLs, we identified eQTLs with significantly different effects between sexes by fitting a linear
regression model and testing for a significant genotype-by-sex (G×S) interaction (11). Across the
44 GTEx tissues shared among sexes, we identified 369 sb-eQTLs (FDR ≤ 25%), characterized
further in (23). Sex-biased eQTL discovery had a modest correlation with tissue sample size
(Spearman’s rho = 0.39, p = 0.03), with most sb-eQTLs discovered in breast but also in muscle,
skin and adipose tissues. In some cases, the cis-eQTL signal — identified with males and females
combined — seems to be driven exclusively by one sex. For example, the cis-eQTL association of
rs2273535 with the gene AURKA in skeletal muscle (cis-eQTL p = 6.92x1024) is correlated with
sex (pG×S = 9.28x10-12, Storey qG×S = 1.07x10-7, AE validation p = 1.15x10-11) and present only in
males (figs. 2d, S12). AURKA is a member of the serine/threonine kinase family involved in mitotic
chromosomal segregation that has been widely studied as a risk factor in several cancers (24-27)
and has been recently shown to be involved in muscle differentiation (28).
We also characterized population-biased cis-eQTLs (pb-eQTLs), where a variant’s
molecular effect on gene expression differs between individuals of European and African ancestry,
controlling for differences in allele frequency and Linkage Disequilibrium (LD) (11). Analyzing
31 tissues with sample sizes >20 in both populations, we mapped genes with a different eQTL
effect size measured by aFC. After applying stringent filters to remove differences potentially
explained by LD or other artifacts (fig. S13a), we identified 178 pb-eQTLs for 141 eGenes (FDR
≤ 25%) that show a moderate degree of validation in allele-specific expression data (fig. S13, table
S10). While some of the pb-eQTL effects are tissue-specific, there are also effects that are shared
across most tissues (fig. S13). Figure 2e shows an example of a pb-eQTL for the SLC44A5 gene
involved in transport of sugars and amino acids, and expressed at different levels between
epidermis of lighter and darker skin (reconstructed in vitro) (29, 30). In Europeans, the derived
allele of rs4606268 decreases expression of the gene in esophagus mucosa (aFC = -4.82), but this
effect is significantly lower in African Americans (aFC = -2.85, permutation p-value = 1.2x10-3,
AE validation p = 0.002, fig. S13)
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This relative paucity of both sex- and population-biased cis-eQTLs reflects the fact that
they are challenging to identify and there are few with large effects, but that they can provide
insights in to sex- or population-specific regulatory effects on gene expression.
Fine-mapping
A major challenge of all genetic association studies is to distinguish the causal variants
from their LD proxies. We applied three different statistical fine-mapping methods — CaVEMaN
(31), CAVIAR (32), and dap-g (16) — to infer likely causal variants of cis-eQTLs in each tissue
(fig. 3a) (11). For many cis-eQTLs the causal variant can be mapped with a high probability to a
handful of candidates: the 90% credible set for each cis-eQTL consists of variants that include the
causal variant with 90% probability; using dap-g, we identified a median of 6 variants in the 90%
credible set for each cis-eQTL (fig. S14). Furthermore, 9.3% of the cis-eQTLs have a variant with
a posterior probability > 0.8 according to dap-g, indicating a single likely causal variant for those
cis-eQTLs. We defined a consensus set of 24,740 cis-eQTLs across all tissues (7,709 unique
variants), for which the posterior probability was >0.8 across all three methods (fig. S15). Fine-
mapped variants were significantly higher enriched among experimentally validated causal
variants from MPRA (33) and SuRE (34) data, compared to the lead eVariant across all eGenes.
The highest enrichment was observed for the consensus set although with overlapping confidence
intervals (fig. 3b). This demonstrates how careful fine-mapping facilitates the identification of
likely causal regulatory variants.
Knowing the likely causal variant enables greater insights into the molecular mechanisms
of individual eQTLs, including the mechanisms of their tissue-specific effects. Figure 3c shows an
example of an eQTL for the gene CBX8 that colocalizes with breast cancer risk and birth weight
(posterior probability 0.68 for both in lung). One of the three variants in the confident set overlaps
the binding site and disrupts the motif of the transcription factor EGR1 (1) (fig. S16). The role of
EGR1 as an upstream driver of this eQTL is further supported by a cross-tissue correlation of the
effect size of the eQTL and the expression level of EGR1 (Spearman’s rho = -0.69) (fig. 3d).
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Figure 3. Fine mapping of cis-eQTLs. (A) Number of eGenes per tissue with variants fine-mapped with >0.5
posterior probability of causality, based on three methods. The overall number of eGenes with at least one fine-mapped
eVariant increases with sample size for all methods. However, this increase is in part driven by better statistical power
to detect small effect size cis-eQTLs (aFC or allelic fold change ≤1 in log2 scale) with larger sample sizes, and the
proportion of well fine-mapped eGenes with small effect sizes increases more modestly with sample size (bottom vs.
top panels), indicating that such cis-eQTLs are generally more difficult to fine-map. (B) Enrichment of variants among
experimentally validated regulatory variants, shown for the cis-eVariant with the best p-value (top eVariant), and those
with posterior probability of causality >0.8 according to each of the three methods individually or all of them
(consensus). Error bars: 95% CI (C) The cis-eQTL signal for CBX8 is fine-mapped to a credible set of three variants
(red and purple diamonds), of which rs9896202 (purple diamond) overlaps a large number of transcription factor
binding sites in ENCODE ChIP-seq data and disrupts the binding motif of EGR1. (D) The potential role of EGR1
binding driving this cis-eQTL is further supported by correlation between EGR1 expression and the CBX8 cis-eQTL
effect size across tissues.
Functional mechanisms of QTL associations
Quantitative trait data from multiple molecular phenotypes, integrated with the regulatory
annotation of the genome and GWAS data (table S3), offer a powerful way to understand the
molecular mechanisms and phenotypic consequences of genetic regulatory effects. As expected,
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cis-eQTLs and cis-sQTLs are significantly enriched in functional elements of the genome (fig. 4a).
While the strongest enrichments are driven by variant classes that lead to splicing changes or
nonsense-mediated decay, these account for relatively few variants. Cis-sQTLs have significant
enrichments almost entirely in transcribed regions, while cis-eQTLs are significantly enriched in
transcriptional regulatory elements as well. Previous studies (4, 35) have indicated that cis-eQTL
and cis-sQTL effects on the same gene are typically driven by different genetic variants. This is
corroborated by the GTEx v8 data, where the overlap of cis-eQTL credible sets of likely causal
variants, based on CAVIAR, have only a 12% overlap with cis-sQTL credible sets (fig. S17).
Functional enrichment of overlapping and non-overlapping cis-eQTLs and cis-sQTLs, based on
stringent LD filtering, showed that the patterns characteristic for each type — such as enrichment
of cis-eQTL in enhancers and cis-sQTLs in splice sites — are even stronger for distinct loci (fig.
S17).
We hypothesized that eVariants and their target eGenes in cis are more likely to be in the
same topologically associated domains (TADs) that allow chromatin interactions between more
distant regulatory regions and target gene promoters (36). To test this, we analyzed TAD data from
ENCODE (1) and cis-eQTLs from matching GTEx tissues (table S3). Compared to matching
random variant-gene pairs and controlling for distance from the transcription start site, cis-
eVariant-eGene pairs were significantly enriched for being in the same TAD (median log odds
1.52; all p<10-12) (fig.S18).
Trans-eQTLs are significantly enriched in regulatory annotations that suggest both pre-
and post-transcriptional mechanisms (fig. 4b). Unlike cis-eQTLs, trans-eQTLs are strongly
enriched in CTCF binding sites, suggesting that disruption of CTCF binding may underlie distal
genetic regulatory effects, potentially via its effect on interchromosomal chromatin interactions
(36). trans-eQTLs have also been shown to be partially driven by cis-eQTLs (37, 38). Indeed, we
observed a significant enrichment of lead trans-eVariants tested in cis being also cis-eVariants in
the same tissue (5.9x; two-sided Fisher’s exact test p = 5.03x10-22, fig. 4c). Lack of analogous
strong enrichment suggests that cis-sQTLs are less important contributors to trans-eQTLs (p =
0.064), and trans-sVariants had no significant enrichment of either cis-eQTLs (p = 0.051) or cis-
sQTLs (p = 0.53). A further demonstration of the important contribution of cis-eQTLs to trans-
eQTLs is that, based on mediation analysis, 77% of lead trans-eVariants that are also cis-eVariants
appear to act through the cis-eQTL (figs. 4d, S19). Colocalization of cis-eQTLs and trans-eQTLs
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was widespread and often tissue-specific, with figure 4e showing cis-eQTLs with at least ten
nominally significant colocalized trans-eQTLs each (PP4 > 0.8 and trans-eQTL p-value < 10-5),
pinpointing how local effects on gene expression can potentially lead to downstream regulatory
effects across the genome (fig. S20, table S15).
Figure 4. Functional mechanisms of genetic regulatory effects. QTL enrichment in functional annotations for (A)
cis-eQTLs and cis-sQTLs and for (B) trans-eQTLs. cis-QTL enrichment is shown as mean ± s.d. across tissues; trans-
eQTL enrichment as 95% C.I. (C) Enrichment of lead trans-e/sVariants tested in cis being also cis-e/sVariants in the
same tissue. * denotes significant enrichment, p < 10-21. (D) Proportion of trans-eQTLs that are significant cis-eQTLs
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or mediated by cis-eQTLs. (E) Trans associations of cis-mediating genes identified through colocalization (PP4 > 0.8
and nominal association with discovery trans-eVariant p < 10-5). Top: associations for four Thyroid cis-eQTLs
(indicated by gene names); bottom: cis-mediating genes with ≥5 colocalizing trans-eQTLs.
Genetic regulatory effects mediate complex trait associations
In order to analyze the role of regulatory variants in genetic associations for human traits,
we first asked whether variants in the GWAS catalog were enriched for significant QTLs,
compared to all variants tested for QTLs (11). We observed a 1.46-fold enrichment for cis-eQTLs
(63% vs 43%) and 1.86-fold enrichment for cis-sQTLs (37% vs 20%). The enrichment was even
stronger, 6.97-fold (0.029% vs 0.0042%) for trans-eQTLs, consistent with other analyses (39)
(figs. 5a, S21-22, tables S5-6).
This approach does not leverage the full power of genome-wide GWAS and QTL genetic
association statistics, nor account for LD contamination, a situation wherein the causal variants for
QTL and GWAS signals are distinct but LD between the two causal variants can suggest a false
functional link (40). Hence, for subsequent analyses (below) we selected 87 Genome Wide
Association Studies (GWAS) representing a broad array of binary and continuous complex traits
that have summary results available in the public domain (11, 41) (tables S4, S11), and cis-QTL
statistics calculated from the European subset of GTEx donors to match the ancestry of GWAS
studies (fig. S24). Analyses described were performed for all pairwise combinations of 87
phenotypes and 49 tissues, and are summarized using an approach that accounts for similarity
between tissues and variable standard errors of the QTL effect estimates, driven mainly by tissue
sample size (fig. S22, (11)).
To analyze the mediating role of cis-regulation of gene expression on complex traits (35,
42), we used two complementary approaches, QTLEnrich (43) and Stratified LD score regression
(S-LDSC) (11). To rule out the possibility that enrichment is driven by specific features of cis-
QTLs such as allele frequency, distance to the transcription start site, or local level of LD (number
of LD proxy variants; r2 ≥ 0.5), we used QTLEnrich. We found a 1.43-fold (SE=0.04) and 1.52-
fold (SE=0.04) enrichment of trait associations among best cis-eQTLs and cis-sQTLs,
respectively, adjusting for enrichment among matched null variants (fig. 5a, tables S7). The fact
that these enrichment estimates differ little from those derived from the GWAS catalog overlap
(above), even after accounting for the potential confounders, indicates how relatively robust these
estimates are. Next, we used S-LDSC adjusting for functional annotations (44) to confirm the
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robustness of these results and to analyze how GWAS enrichment is affected by the causal
e/sVariant being typically unknown (11). We computed the heritability enrichment of all cis-
QTLs, fine-mapped cis-QTLs (in 95% credible set and posterior probability > 0.01 from dap-g),
and fine-mapped cis-QTLs with maximum posterior inclusion probability as continuous
annotation (MaxCPP) (45) (fig. 5a). The largest increase in GWAS enrichment was for likely
causal cis-QTL variants (11.1-fold (SE=1.2) for cis-eQTLs and 14.2-fold (SE=2.4) for and cis-
sQTLs, for the continuos annotation), which is strong evidence of shared causal effects of cis-
QTLs and GWAS, and for the importance of fine-mapping.
Joint enrichment analysis of cis-eQTLs and cis-sQTLs shows an independent contribution
to complex trait variation from both (fig. S23, (11)), consistent with their limited overlap (fig.
S17). The relative GWAS enrichments of cis-sQTLs and cis-eQTLs were similar (fig. 5a; not
significant for the robust QTLEnrich and LDSC analyses), but the larger number of cis-eQTLs
discovered (fig. 2a) suggests a greater aggregated contribution of cis-eQTLs.
To provide functional interpretation of the 5,385 significant GWAS associations in 1,167
loci from approximately independent LD blocks (46) across the 87 complex traits, we performed
colocalization with enloc (16) to quantify the probability that the cis-QTL and GWAS signals share
the same causal variant. We also assessed the association between the genetically regulated
component of expression or splicing and complex traits with PrediXcan (11, 41, 47). Both methods
take multiple independent cis-QTLs into account, which is critical in large cis-eQTL studies such
as GTEx with widespread allelic heterogeneity. Of the 5,385 GWAS loci, 43% and 23% were
colocalized with a cis-eQTL and cis-sQTL, respectively (fig. 5b). A large proportion of colocalized
genes coincide with significant PrediXcan trait associations with predicted expression or splicing
(median of 86% and 88% across phenotypes respectively, figs. S25-S28, tables S8). Together,
these results suggest target genes and their potential molecular changes for thousands of GWAS
loci.
Having multiple independent cis-eQTLs for a large number of genes allowed us to test
whether mediated effects of primary and secondary cis-eQTLs on phenotypes — the ratio of
GWAS and cis-eQTL effect sizes — are concordant. To make sure that concordance is not driven
by residual LD between primary and secondary signals, we used LD-matched cis-eGenes with low
colocalization probability as controls (11, 41), and observed a significant increase in primary and
secondary cis-eQTL concordance for colocalized genes (p-value < 10-30; fig. 5c). Additionally,
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colocalization of a cis-eQTL increased the colocalization of an independent cis-sQTL in the same
locus (OR = 4.27, p < 10-16), and correspondingly colocalization of a cis-sQTL increased cis-eQTL
colocalization (OR = 4.54 p < 10-16; fig. S29). This indicates that multiple regulatory effects for
the same gene often mediate the same complex trait associations. Furthermore, genes with
suggestive rare variant trait associations in the UK Biobank (48) have a substantially increased
proportion of colocalized eQTLs for the same trait (fig. 5d), showing concordant trait effects from
rare coding and common regulatory variants (49). These genes, as well as those with multiple
colocalizing cis-QTLs, represent bona fide disease genes with multiple independent lines of
evidence.
The growing number of genome and phenome studies has revealed extensive pleiotropy,
where the same variant or locus associates with multiple organismal phenotypes (50). We sought
to analyze how this phenomenon can be driven by gene regulatory effects. First, we calculated the
number of cis-eGenes of each fine-mapped and LD-pruned cis-eVariant per tissue at local LFSR
< 5%, with cross-tissue smoothing of effect sizes with mashr (11, 51). We observed that a median
of 57% of variants were associated with more than one gene per tissue, typically co-occurring
across tissues, indicating widespread regulatory pleiotropy. Using a binary classification of cis-
eVariants with regulatory pleiotropy defined as those associated with more than one gene, we
observed that they are more significantly associated with complex traits compared to matched cis-
eVariants (fig. S30). This could be due to the fact that if a variant regulates multiple genes, there
is a higher probability that at least one of them affects a GWAS phenotype. However, cis-eVariants
with regulatory pleiotropy also have higher GWAS complex trait pleiotropy (50) than cis-
eVariants with effects on a single gene (fig. 5e). This observation suggests a mechanism for
complex trait pleiotropy of genetic effects where the expression of multiple genes in cis, rather
than a single eGene effect, translates into diverse downstream physiological effects. Furthermore,
GWAS pleiotropy is higher for tissue-shared (41) than tissue-specific cis-eQTLs, indicating that
regulatory effects affecting multiple tissues are more likely to translate to diverse physiological
traits (fig. 5e).
Cis- and trans-eQTLs can provide insights into potential mechanisms and effects of trait-
associated variants. In one such example, rs1775555 on chr10p14 is a fibroblast-specific cis-eQTL
for GATA3 (p=7.4x10-70) and a lincRNA gene GATA3-AS1 (p=1.8x10-45) and a trans-eQTL for
MSTN on chromosome 2, which encodes a TGF-β ligand secreted protein (fig. S31) and has a role
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in muscle growth and also the immune system (52). GATA3 is a transcription factor known to
regulate a range of processes of immune system including T cell development, Th2 differentiation,
and immune cell homeostasis and survival (53). The cis- (GATA3) and trans-eQTL (MSTN)
associations colocalized (PP4 > 0.99) in fibroblasts, and mediation analysis supports that the effect
of rs1775555 on MSTN is mediated through GATA3 (p=2.1x10-22, (11)). We also found that the
cis- and trans-eQTL effect of rs1775555 colocalized with associations for multiple immune traits,
including combined eosinophil and basophil counts, hayfever/eczema, and asthma (PP4 > 0.97 for
all eQTL-trait combinations; fig. S31). DTNA, C4orf26, GK5, HSD11B1, SLC44A1, ARHGAP25,
MAN2A1 are additional genes that showed trans association with this variant (FDR 10%, corrected
for number of cross-chromosomal genes tested for association with rs1775555). While the causal
relationships are not obvious, this locus demonstrates broad impact on multiple phenotypes and
both local and distal gene expression.
Figure 5. Regulatory mechanisms of GWAS loci. (A) GWAS enrichment of cis-eQTLs, cis-sQTLs, and trans-
eQTLs measured with different approaches: enrichment based on GWAS summary statistics of the most significant
cis-QTL per eGene/sGene with QTLEnrich and LD Score regression with all significant cis-QTLs (S-LDSC all cis-
QTLs), simple QTL overlap enrichment with all GWAS catalog variants, and LD Score regression with fine-mapped
cis-QTLs in the 95% credible set (S-LDSC credible set) and using posterior probability of causality as a continuous
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annotation (S-LDSC causal posterior). Enrichment is shown as mean and 95% CI. (B) Number of GWAS loci linked
to e/sGenes through colocalization (ENLOC) and association (PrediXcan), aggregated across tissues. (C)
Concordance of mediated effects among independent cis-eQTLs for the same gene is shown for different levels of
colocalization probability, which is used as a proxy for the gene's causality. As the null, we show the concordance for
LD matched genes without colocalization. (D) Proportion of colocalized cis-eQTLs with a matching phenotype for
genes with different level of rare variant trait association in the UK Biobank. (E) Horizontal GWAS trait pleiotropy
score distribution for cis-eQTLs that regulate multiple vs. a single gene (left), and for cis-eQTLs that are tissue-shared
vs specific.
Tissue-specificity of genetic regulatory effects
The GTEx data provide a unique opportunity to study patterns and mechanisms of tissue-
specificity of the transcriptome and its genetic regulation. Pairwise similarity of GTEx tissues was
quantified using gene expression and splicing, as well as allelic expression, eQTLs in cis and trans,
and cis-sQTLs (figs. 6a, S34, (11)). These show highly consistent patterns of tissue relatedness,
indicating that the same biological processes that drive transcriptome similarity also control tissue
sharing of genetic effects (fig. 6b). As seen in earlier versions of the GTEx data (9, 10), the brain
regions form a separate cluster, and testis, LCLs, whole blood, and sometimes liver tend to be
outliers, while most other organs have a notably high degree of similarity between each other. This
indicates that blood is far from an ideal proxy for most tissues, but that some other relatively
accessible tissues, such as skin, may be better at capturing molecular effects in other tissues.
The overall tissue specificity of QTLs (11) follows a U-shaped curve recapitulating
previous GTEx analyses (9, 10), where genetic regulatory effects tend to be either highly tissue-
specific or highly shared (fig. 6c), with trans-eQTLs being more tissue-specific than cis-eQTLs
(fig. S33). Cis-sQTLs appear to be significantly more tissue specific than cis-eQTLs when
considering all mapped cis-QTLs, but this pattern is reversed when considering only those cis-
QTLs where the gene or splicing event is quantified in all tissues (figs. 6c, S32). This indicates
that splicing measures are more tissue-specific than gene expression, but genetic effects on splicing
tend to be more shared, consistent with pairwise tissue sharing patterns (fig. S34). This is important
for understanding effects that disease-causing splicing variants may have across tissues, and for
validation of splicing effects in cell lines that rarely are an exact match to cells in vivo. Next, we
analyzed the sharing of allelic expression (AE) across multiple tissues of an individual, which is a
sensitive metric of sharing of any heterozygous regulatory variant effects in that individual and
has been particularly useful for analysis of rare, potentially disease-causing variants (54). Using a
clustering approach (11), we found that in 97.4% of the cases, AE across all tissues forms a single
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cluster. This suggests that in AE analysis, different tissues are often relatively good proxies for
one another, provided that the gene of interest is expressed in the probed tissue (fig. S35).
We next computed the cross-tissue correlation of eQTL effect size and eGene expression
level — often a proxy for gene functionality — and discovered that 1,971 cis-eQTLs (7.4%; FDR
5%) had a significant and robust correlation between eGene expression and cis-eQTL effect size
across tissues (fig. 6d, S36). These correlated cis-eQTLs are split nearly evenly between negative
(937) and positive (1,034) correlations. Thus, the tissues with the highest cis-eQTL effect sizes are
equally likely to be among tissues with higher or lower expression levels for the gene. Trans-
eQTLs show a different pattern, being typically observed in tissues with high expression of the
trans-eGene relative to other tissues (fig. S36). These observations raise the question how to
prioritize the relevant tissues for eQTLs in a disease context. To address this, we chose a subset of
GWAS traits where previous studies provide a strong prior for the likely relevant tissue(s) (table
S12). Analyzing colocalized cis-eQTLs for 1,778 GWAS loci (11), we discovered that the relevant
tissues were modestly but significantly enriched in having high expression and effect sizes
(p<1.5x10-4) (figs. S37-38, table S9). This indicates that both effect size and gene expression level
are important in the interpretation of the tissue context where an eQTL may have downstream
phenotypic effects.
The diverse patterns of QTL tissue-specificity raise the question of what molecular
mechanisms underlie the ubiquitous regulatory effects of some genetic variants and the highly
tissue-specific effects of others. To gain insight into this question, we modeled cis-eQTL and cis-
sQTL tissue specificity using logistic regression as a function of the lead eVariant’s genomic and
epigenomic context (11). Cis-QTLs where the top eVariant was in a transcribed region had overall
higher sharing than those in classical transcriptional regulatory elements, indicating that genetic
variants with post- or co-transcriptional expression or splicing effects have more ubiquitous effects
(fig. 6e). Canonical splice and stop gained variant effects had the highest probability of being
shared across tissues, which may benefit disease-focused studies relying on likely gene-disrupting
variants. We also considered whether varying regulatory activity between tissues contributed to
tissue-specificity of genetic effects, and found that shared chromatin state between the discovery
and query tissues was associated with increased probability of cis-eQTL sharing and vice-versa
(fig. 6f). cis-eQTLs and cis-sQTLs followed similar patterns. Since cis-sQTLs are more enriched
in transcribed regions and likely post-transcriptional mechanisms (fig. 4a), this is likely to
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contribute to their higher overall degree of tissue-sharing (fig. 6c). In comparison to cis-eQTLs,
cis-sQTLs are indeed more often located in regions where regulatory effects are shared. These data
offer a possibility to predict if an cis-eQTL observed in a GTEx tissue is active in another tissue
of interest, based on its annotation and properties in the discovery tissue (11). After incorporating
additional features including cis-QTL effect size, distance to transcription start site, and
eGene/sGene expression levels, we obtain reasonably good predictions of whether a cis-QTL is
active in a query tissue (median AUC = 0.779 and 0.807, min = 0.703 and 0.721, max = 0.807 and
0.875 for cis-eQTLs and cis-sQTLs, respectively; fig. S39). This suggests that it is possible to
extrapolate the GTEx cis-eQTL catalog to additional tissues or, for example, developmental stages
where population-scale data for QTL analysis are particularly difficult to collect.
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Figure 6. Tissue-specificity of cis-QTLs. (A) Tissue clustering based on pairwise Spearman correlation of cis-eQTL
effect sizes. (B) Similarity of tissue clustering across core data types quantified using median pairwise Rand index
calculated across tissues. (C) Tissue activity of cis expression and splicing QTLs, where an eQTL was considered
active in a tissue if it had a mashr local false sign rate (LFSR, equivalent to FDR) of < 5%. This is shown for all cis-
QTLs and only those that could be tested in all 49 tissues (red and blue). (D) Spearman correlation (corr.) between
cis-eQTL effect size and eGene expression level across tissues. cis-eQTL counts are shown for those not tested due
to low expression level, tested but without significant (FDR < 5%) correlation (uncorrelated), a significant correlation
but effect sizes crossed zero which made the correlation direction unclear (uninterpretable), positively correlated, and
negatively correlated. (E-F) The effect of genomic function on cis-QTL tissue sharing modeled using logistic
regression, using functional annotations (E) and chromatin state (F). CTCF Peak, Motif, TF Peak, and DHS indicate
if the cis-QTL lies in a region annotated as having one of these features in any of the Ensembl Regulatory Build
tissues. For chromatin states, model coefficients are shown for the discovery and replication tissues that have the same
or different chromatin states.
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From tissues to cell types
The GTEx tissue samples consist of heterogeneous mixtures of multiple cell types. Hence,
the RNA extracted and QTLs mapped from these samples reflect a composite of effects that may
vary across cell types and may mask cell type-specific mechanisms. To characterize the effect of
cell type heterogeneity on analyses from bulk tissue, we used the xCell method (55) to estimate
the enrichment of 64 reference cell types from the bulk expression profile of each sample (11).
The resulting enrichment scores were generally biologically meaningful, with for example
myocytes enriched in heart left ventricle and skeletal muscle, hepatocytes enriched in liver, and
various blood cell types enriched in whole blood, spleen, and lung, which is known to harbor a
large leukocyte population (fig. S40). As discussed in more detail in (56), these results need to be
interpreted with caution given the scarcity of validation data and quality and quantity of cell type
reference data sets. Nonetheless, the pairwise relatedness of GTEx tissues derived from their cell
type composition is highly correlated with tissue-sharing of regulatory variants (figs. 5b, S41,
S34), suggesting similarity of regulatory variant activity between tissue pairs may often be due to
the presence of similar cell types, and not necessarily shared regulatory networks within cells. This
highlights the key role that characterizing cell type diversity will have, not only for understanding
tissue biology, but the underlying role of genetic variation as well.
Enrichment of many cell types shows inter-individual variation within a given tissue (56).
In eQTL analysis, this variation can be leveraged to identify cis-eQTLs and cis-sQTLs with cell
type specificity by extending the QTL model to include an interaction between genotype and cell
type enrichment (11, 57). We applied this approach to seven tissue-cell type pairs that were chosen
based on having robustly quantified cell types and the tissue where each cell type was most
enriched (fig. 7a; an additional 36 pairs are described in (56)). Power to discover cell type
interacting cis-eQTLs and cis-sQTLs (ieQTLs and isQTLs, respectively) varied as a function of
tissue heterogeneity and complexity as well as sample size (56). We notably identified 1120
neutrophil ieQTLs in whole blood and 1087 epithelial cell ieQTLs in transverse colon (fig. 1a); of
these, 76 and 229 respectively, involved an eGene for which no QTL was detected in bulk tissue.
eQTLs from purified neutrophils of an external data set (58) had higher neutrophil ieQTL effect
sizes than eQTLs from other blood cell types (fig. S42). For other cell types external replication
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data was lacking. Thus, we verified the robustness of the ieQTLs by the allelic expression
validation approach that was used for sex- and population-biased cis-eQTL analyses: for ieQTL
heterozygotes, we calculated the Spearman correlation of cell type enrichment and ieQTL effect
size from AE data, and observed a high validation rate (56). It is important to note that ie/isQTLs
should not be considered cell type-specific QTLs, because the enrichment of any cell type may be
(anti-)correlated with other cell types (fig. S43). While full deconvolution of cis-eQTL effects
driven by specific cell types remains a challenge for the future, ieQTLs and isQTLs can be
interpreted as being enriched for cell type-specific effects. In most subsequent analyses to
characterize the properties of ieQTLs and isQTLs, we focused on the neutrophil ieQTLs, which
are numerous and supported by external replication data.
Analysis of functional enrichment of neutrophil ieQTLs and isQTLs shows that these
largely follow the enrichment patterns observed for bulk tissue cis-QTLs (fig. 7b), with ieQTLs
more strongly enriched in promoter flanking regions and enhancers, which are known to be major
drivers of cell type specific regulatory effects (2). We observed similar patterns for epithelial cell
ieQTLs (fig. S44).
We hypothesized that the widespread allelic heterogeneity observed in the bulk tissue cis-
eQTL data is partially driven by an aggregate signal from cis-eQTLs that are each active in a
different cell type present in the tissue. Indeed, the number of cis-eQTLs per gene is higher for
ieGenes than for standard eGenes in several tissues (fig. 7c). While differences in power could
contribute to this pattern, it is strongly corroborated by eGenes that have independent cis-eQTLs
(LD < 0.05) in five purified blood cell types (58) also showing an increased amount of allelic
heterogeneity in GTEx whole blood (fig. 7c,d). Thus, insights into cell type specificity provides
new understanding of mechanisms of genetic architecture of gene expression, with promise of
improved resolution into complex patterns of allelic heterogeneity when effects manifesting in
different cell types can be distinguished from each other.
Next, we analyzed how cell type interacting cis-QTLs contribute to the interpretation of
regulatory variants underlying complex disease risk. GWAS colocalization analysis of neutrophil
ieQTLs (11) revealed multiple loci (111, ~32%) that colocalize only with ieQTLs and not with
whole blood cis-eQTLs (fig. 7e), even though 75% (42/56) of the corresponding eGenes have both
cis-eQTLs and ieQTLs. Improved resolution into allelic heterogeneity appears to contribute to this,
with fig. S45 showing an example of a locus where the absence of colocalization between a platelet
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count GWAS signal and bulk tissue cis-eQTL for SPAG7 appears to be due to the whole blood
signal being an aggregate of multiple independent signals. The neutrophil ieQTL analysis uncovers
a specific signal that mirrors the GWAS association, suggesting that platelet counts are affected
by SPAG7 expression only in specific cell type(s). Thus, in addition to novel colocalizations
pinpointing potential causal genes, ieQTL analysis has the potential to provide insights into cell
type specific mechanisms of complex traits.
Figure 7. Cell type interacting cis-eQTLs and cis-sQTLs. (A) Number of cell type interacting cis-eQTLs and cis-
sQTLs (ieQTLs and isQTLs, respectively) discovered in seven tissue-cell type pairs, with shading indicating whether
the ieGene or isGene was discovered by cis-eQTL/cis-sQTL analysis in bulk tissue. Colored dots are proportional to
sample size. (B) Functional enrichment of neutrophil ieQTLs and isQTLs compared to cis-eQTLs and cis-sQTLs from
whole blood. (C) Proportion of conditionally independent cis-eQTLs per eGene, for eGenes that do or do not have
ieQTLs in GTEx, and for eGenes that have shared (= eQTLs) or non-shared (≠ eQTLs) cis-eQTL across five sorted
blood cell types. (D) Whole blood cis-eQTL p-value landscape for NCOA4, for the standard analysis (top row,
Unconditional) and for two independent cis-eQTLs (bottom rows). In a data set of 5 sorted cell types (58), analyses
of all cell types yielded a lead eVariant, rs2926494 (left), which is in high LD with the first independent cis-eQTL but
not the second. The lead variant in monocyte cis-eQTL analysis, rs10740051, is in high LD with the second conditional
cis-eQTL, indicating that this cis-eQTL is active specifically in monocytes. Thus, the full GTEx whole blood cis-
eQTL pattern and allelic heterogeneity is composed of cis-eQTLs that are active in different cell types. (E) COLOC
posterior probability (PP4) of GWAS colocalization with whole blood ieQTLs and eQTLs of the same eGene for 36
GWAS traits.
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Discussion
The GTEx v8 data release represents the deepest survey of both intra- and inter-individual
transcriptome variation across a large number of tissues. With 838 donors and 15,253 samples, we
have created a comprehensive catalog of genetic variants that influence gene expression and
splicing in cis. The fine-mapping data of GTEx cis-eQTLs provides a catalog of thousands of likely
causal functional variants – the largest resource of this type. While trans-QTL discovery, as well
as characterization of sex-specific and population-specific genetic effects, are still limited by
sample size, analyses of the V8 data provide important insights into each. Cell type interacting
cis-eQTLs and cis-sQTLs, mapped using computational estimates of cell type enrichment,
constitute an important addition to the GTEx resource. The strikingly similar tissue-sharing
patterns across these data types suggests shared biology from cell type composition to
transcriptome variation and genetic regulatory effects. Our results indicate that shared cell types
between tissues may be a key factor behind tissue-sharing of genetic regulatory effects, which will
constitute a key challenge to tackle in the future. Finally, GWAS colocalization with cis-eQTLs
and cis-sQTLs provides rich opportunities for further functional follow-up and characterization of
regulatory mechanisms of GWAS associations.
Given the very large number of cis-eQTLs, the extensive allelic heterogeneity – multiple
independent regulatory variants affecting the same gene – is unsurprising. With well-powered cis-
QTL mapping, it becomes possible and important to describe and disentangle these effects; the
assumption of a single causal variant in a cis-eQTL locus no longer holds true for data sets of this
scale. Similarly, we highlight cis-eQTL and cis-sQTL effects on the same gene, typically driven
by distinct causal variants. The joint complex trait contribution of independent cis-eQTLs and cis-
sQTLs, and cis-eQTLs and rare coding variants for the same gene highlights how different genetic
variants and functional perturbations can converge at the gene level to similar physiological
effects. This orthogonal evidence pinpoints gold-standard disease genes, and could be leveraged
to build allelic series, a powerful tool for estimating dosage-risk relationship for the purposes of
drug development (59). Finally, we provide mechanistic insights into the cellular causes of allelic
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heterogeneity, showing the separate contributions from cis-eQTLs active in different cell types to
the combined signal seen in a bulk tissue sample. With evidence that this increased cellular
resolution improves colocalization in some loci, cell type specific analyses appear particularly
promising for finer dissection of genetic association data.
Integration of GTEx QTL data and functional annotation of the genome provides powerful insights
into the molecular mechanisms of transcriptional and post-transcriptional regulation that affect
gene expression levels and splicing. A large proportion of cis-eQTL effects are driven by genetic
perturbations in classical regulatory elements of promoters and enhancers, with an enrichment of
tissue-specific and cell-type interacting cis-eQTLs in enhancers and related elements that thus
contribute to context-specific genetic effects. Furthermore, we demonstrate that regulatory
elements and transcription factors with variable activity across tissues and cell types modify cis-
QTL effect sizes. While cis-eQTLs are enriched for a wide range of functional regions, the vast
majority of cis-sQTL are located in transcribed regions, with likely co-/post-transcriptional
regulatory effects. Interestingly, these appear to be less tissue-specific, which likely contributes to
the higher tissue-sharing of cis-sQTLs than cis-eQTLs.
Approximately half of the observed trans-eQTLs are mediated by cis-eQTLs, demonstrating how
local genetic regulatory effects can translate to effects at the level of cellular pathways. All types
of QTLs that were studied are strong mediators of genetic associations to complex traits, with a
higher relative enrichment for cis-sQTLs than cis-eQTLs, with trans-eQTLs having the highest
enrichment of all (35). With large GWAS/PheWAS studies having uncovered extensive pleiotropy
of complex trait associations, the GTEx data provide important insights into its molecular
underpinnings: variants that affect the expression of multiple genes and multiple tissues have a
higher degree of complex trait pleiotropy, indicating that some of the pleiotropy arises at the
proximal regulatory level. Dissecting this complexity, and pinpointing truly causal molecular
effects that mediate specific phenotype associations will be a considerable challenge for the future.
This study of the GTEx v8 data set has provided essential insights into genetic regulatory
architecture and functional mechanisms. The extensive catalog of QTLs and associated data sets
of annotations, cell types enrichments, and GWAS summary statistics provides rich material that
requires careful interpretation for insights into the biology of gene regulation and functional
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mechanisms of complex traits. We have demonstrated how QTL data can be used to inform on
multiple layers of GWAS interpretation: mapping of likely causal variants, proximal regulatory
mechanisms, target genes in cis, pathway effects in trans, in the context of multiple tissues and
cell types. However, our understanding of genetic effects on cellular phenotypes is far from
complete. We envision that further investigation into genetic regulatory effects in specific cell
types, study of additional tissues and developmental time points not covered by GTEx,
incorporation of a diverse set of molecular phenotypes, and continued investment in increasing
sample sizes from diverse populations will continue to provide transformative scientific
discoveries.
Data availability
All GTEx protected data are available via dbGaP (accession phs000424.v8). Access to the raw
sequence data is now provided through the AnVIL platform
(https://gtexportal.org/home/protectedDataAccess). The GTEx V8 non-protected data are
available on the GTEx Portal, with multiple data views and analysis results publicly available on
the Portal (www.gtexportal.org), as well as in the UCSC and Ensembl browsers. All components
of the single tissue cis-QTL pipeline are available at https://github.com/broadinstitute/gtex-
pipeline, and analysis scripts are available at https://github.com/broadinstitute/gtex-v8. Residual
GTEx biospecimens have been banked, and remain available as a resource for further studies
(access can be requested on the GTEx Portal, https://www.gtexportal.org/home/samplesPage).
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Authors
Lead Analysts*
François Aguet1#, Alvaro N Barbeira2, Rodrigo Bonazzola2, Andrew Brown3,4, Stephane E Castel5,6, Brian Jo7,8, Silva
Kasela5,6, Sarah Kim-Hellmuth5,6,9, Yanyu Liang2, Meritxell Oliva2,10, Princy Parsana11
Analysts*
Elise Flynn5,6, Laure Fresard12, Eric R Gamazon13,14,15,16, Andrew R Hamel17,1, Yuan He18, Farhad Hormozdiari19,1, Pejman
Mohammadi5,6,20,21, Manuel Muñoz-Aguirre22,23, YoSon Park24,25, Ashis Saha11, Ayellet V Segrè1,17, Benjamin J Strober18,
Xiaoquan Wen26, Valentin Wucher22
Manuscript Working Group*
François Aguet1, Kristin G Ardlie1, Alvaro N Barbeira2, Alexis Battle18,11, Rodrigo Bonazzola2, Andrew Brown3,4,
Christopher D Brown24, Stephane E Castel5,6, Nancy Cox16, Sayantan Das26, Emmanouil T Dermitzakis3,27,28, Barbara E
Engelhardt7,8, Elise Flynn5,6, Laure Fresard12, Eric R Gamazon13,14,15,16, Diego Garrido-Martín22, Nicole R Gay29, Gad Getz1,30,
Roderic Guigó22,31, Andrew R Hamel17,1, Robert E Handsaker32,33,34, Yuan He18, Paul J Hoffman5, Farhad Hormozdiari19,1, Hae
Kyung Im2, Brian Jo7,8, Silva Kasela5,6, Seva Kashin32,33,34, Sarah Kim-Hellmuth5,6,9, Alan Kwong26, Tuuli Lappalainen5,6,
Xiao Li1, Yanyu Liang2, Daniel G MacArthur33,35, Pejman Mohammadi5,6,20,21, Stephen B Montgomery12,29, Manuel Muñoz-
Aguirre22,23, Meritxell Oliva2,10, YoSon Park24,25, Princy Parsana11, John M Rouhana17,1, Ashis Saha11, Ayellet V Segrè1,17,
.CC-BY 4.0 International licenseIt is made available under a
was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which. http://dx.doi.org/10.1101/787903doi: bioRxiv preprint first posted online Oct. 3, 2019;
Matthew Stephens36, Barbara E Stranger2,37, Benjamin J Strober18, Ellen Todres1, Ana Viñuela38,3,27,28, Gao Wang36, Xiaoquan
Wen26, Valentin Wucher22, Yuxin Zou39
Analysis Team Leaders*
François Aguet1, Alexis Battle18,11, Andrew Brown3,4, Stephane E Castel5,6, Barbara E Engelhardt7,8, Farhad Hormozdiari19,1,
Hae Kyung Im2, Sarah Kim-Hellmuth5,6,9, Meritxell Oliva2,10, Barbara E Stranger2,37, Xiaoquan Wen26
Senior Leadership*
Kristin G Ardlie1, Alexis Battle18,11, Christopher D Brown24, Nancy Cox16, Emmanouil T Dermitzakis3,27,28, Barbara E
Engelhardt7,8, Gad Getz1,30, Roderic Guigó22,31, Hae Kyung Im2, Tuuli Lappalainen5,6, Stephen B Montgomery12,29, Barbara E
Stranger2,37
Manuscript Writing Group
François Aguet1, Hae Kyung Im2, Alexis Battle18,11, Kristin G Ardlie1, Tuuli Lappalainen5,6
Corresponding Authors
François Aguet1, Kristin G Ardlie1, Tuuli Lappalainen5,6
GTEx Consortium*
Laboratory and Data Analysis Coordinating Center (LDACC): François Aguet1, Shankara Anand1, Kristin G
Ardlie1, Stacey Gabriel1, Gad Getz1,30, Aaron Graubert1, Kane Hadley1, Robert E Handsaker32,33,34, Katherine H Huang1,
Seva Kashin32,33,34, Xiao Li1, Daniel G MacArthur33,35, Samuel R Meier1, Jared L Nedzel1, Duyen Y Nguyen1, Ayellet
V Segrè1,17, Ellen Todres1
Analysis Working Group (funded by GTEx project grants): François Aguet1, Shankara Anand1, Kristin G Ardlie1,
Brunilda Balliu40, Alvaro N Barbeira2, Alexis Battle18,11, Rodrigo Bonazzola2, Andrew Brown3,4, Christopher D
Brown24, Stephane E Castel5,6, Don Conrad41,42, Daniel J Cotter29, Nancy Cox16, Sayantan Das26, Olivia M de Goede29,
Emmanouil T Dermitzakis3,27,28, Barbara E Engelhardt7,8, Eleazar Eskin43, Tiffany Y Eulalio44, Nicole M Ferraro44,
Elise Flynn5,6, Laure Fresard12, Eric R Gamazon13,14,15,16, Diego Garrido-Martín22, Nicole R Gay29, Gad Getz1,30, Aaron
Graubert1, Roderic Guigó22,31, Kane Hadley1, Andrew R Hamel17,1, Robert E Handsaker32,33,34, Yuan He18, Paul J
Hoffman5, Farhad Hormozdiari19,1, Lei Hou45,1, Katherine H Huang1, Hae Kyung Im2, Brian Jo7,8, Silva Kasela5,6, Seva
Kashin32,33,34, Manolis Kellis45,1, Sarah Kim-Hellmuth5,6,9, Alan Kwong26, Tuuli Lappalainen5,6, Xiao Li1, Xin Li12,
Yanyu Liang2, Daniel G MacArthur33,35, Serghei Mangul43,46, Samuel R Meier1, Pejman Mohammadi5,6,20,21, Stephen B
Montgomery12,29, Manuel Muñoz-Aguirre22,23, Daniel C Nachun12, Jared L Nedzel1, Duyen Y Nguyen1, Andrew B
Nobel47, Meritxell Oliva2,10, YoSon Park24,25, Yongjin Park45,1, Princy Parsana11, Ferran Reverter48, John M Rouhana17,1,
Chiara Sabatti49, Ashis Saha11, Ayellet V Segrè1,17, Andrew D Skol2,50, Matthew Stephens36, Barbara E Stranger2,37,
Benjamin J Strober18, Nicole A Teran12, Ellen Todres1, Ana Viñuela38,3,27,28, Gao Wang36, Xiaoquan Wen26, Fred
Wright51, Valentin Wucher22, Yuxin Zou39
Analysis Working Group (not funded by GTEx project grants): Pedro G Ferreira52,53,54, Gen Li55, Marta Melé56,
Esti Yeger-Lotem57,58
Leidos Biomedical - Project Management: Mary E Barcus59, Debra Bradbury60, Tanya Krubit60, Jeffrey A McLean60,
Liqun Qi60, Karna Robinson60, Nancy V Roche60, Anna M Smith60, Leslie Sobin60, David E Tabor60, Anita Undale60
Biospecimen collection source sites: Jason Bridge61, Lori E Brigham62, Barbara A Foster63, Bryan M Gillard63,
Richard Hasz64, Marcus Hunter65, Christopher Johns66, Mark Johnson67, Ellen Karasik63, Gene Kopen68, William F
Leinweber68, Alisa McDonald68, Michael T Moser63, Kevin Myer65, Kimberley D Ramsey63, Brian Roe65, Saboor
Shad68, Jeffrey A Thomas68,67, Gary Walters67, Michael Washington67, Joseph Wheeler66
Biospecimen core resource: Scott D Jewell69, Daniel C Rohrer69, Dana R Valley69
.CC-BY 4.0 International licenseIt is made available under a
was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which. http://dx.doi.org/10.1101/787903doi: bioRxiv preprint first posted online Oct. 3, 2019;
Brain bank repository: David A Davis70, Deborah C Mash70
Pathology: Mary E Barcus59, Philip A Branton71, Leslie Sobin60
ELSI study: Laura K Barker72, Heather M Gardiner72, Maghboeba Mosavel73, Laura A Siminoff72
Genome Browser Data Integration & Visualization: Paul Flicek74, Maximilian Haeussler75, Thomas Juettemann74,
W James Kent75, Christopher M Lee75, Conner C Powell75, Kate R Rosenbloom75, Magali Ruffier74, Dan Sheppard74,
Kieron Taylor74, Stephen J Trevanion74, Daniel R Zerbino74
eGTEx groups: Nathan S Abell29, Joshua Akey76, Lin Chen10, Kathryn Demanelis10, Jennifer A Doherty77, Andrew P
Feinberg78, Kasper D Hansen79, Peter F Hickey80, Lei Hou45,1, Farzana Jasmine10, Lihua Jiang29, Rajinder Kaul81,82,
Manolis Kellis45,1, Muhammad G Kibriya10, Jin Billy Li29, Qin Li29, Shin Lin83, Sandra E Linder29, Stephen B
Montgomery12,29, Meritxell Oliva2,10, Yongjin Park45,1, Brandon L Pierce10, Lindsay F Rizzardi84, Andrew D Skol2,50,
Kevin S Smith12, Michael Snyder29, John Stamatoyannopoulos81,85, Barbara E Stranger2,37, Hua Tang29, Meng Wang29
NIH program management: Philip A Branton71, Latarsha J Carithers71,86, Ping Guan71, Susan E Koester87, A Roger
Little88, Helen M Moore71, Concepcion R Nierras89, Abhi K Rao71, Jimmie B Vaught71, Simona Volpi90
Acknowledgements
We thank the donors and their families for their generous gifts of organ donation for transplantation, and tissue
donations for the GTEx research project; the Genomics Platform at the Broad Institute for data generation; Jeffrey
Struewing for his support and leadership of the GTEx project; Mariya Khan and Christopher Stolte for the illustrations
in Figure 1; and Ron Do, Daniel Jordan, and Marie Verbanck for providing GWAS pleiotropy scores. This work was
funded by GTEx program grants: HHSN268201000029C (F.A., K.G.A., A.V.S., X.Li., E.T., S.G., A.G., S.A., K.H.H.,
D.Y.N., K.H., S.R.M., J.L.N.), 5U41HG009494 (F.A., K.G.A.), 10XS170 (Subcontract to Leidos Biomedical)
(W.F.L., J.A.T., G.K., A.M., S.S., R.H., G.Wa., M.J., M.Wa., L.E.B., C.J., J.W., B.R., M.Hu., K.M., L.A.S., H.M.G.,
M.Mo., L.K.B.), 10XS171 (Subcontract to Leidos Biomedical) (B.A.F., M.T.M., E.K., B.M.G., K.D.R., J.B.),
10ST1035 (Subcontract to Leidos Biomedical) (S.D.J., D.C.R., D.R.V.), R01DA006227-17 (D.C.M., D.A.D.),
Supplement to University of Miami grant DA006227. (D.C.M., D.A.D.), HHSN261200800001E (A.M.S., D.E.T.,
N.V.R., J.A.M., L.S., M.E.B., L.Q., T.K., D.B., K.R., A.U.), R01MH101814 (M.M-A., V.W., S.B.M., R.G., E.T.D.,
D.G-M., A.V.), U01HG007593 (S.B.M.), R01MH101822 (C.D.B.), U01HG007598 (M.O., B.E.S.), U01MH104393
(A.P.F.), as well as other funding sources: R01MH106842 (T.L., P.M., E.F., P.J.H.), R01HL142028 (T.L., Si.Ka.,
P.J.H.), R01GM122924 (T.L., S.E.C.), R01MH107666 (H.K.I.), P30DK020595 (H.K.I.), UM1HG008901 (T.L.),
R01GM124486 (T.L.), R01HG010067 (Y.Pa.), R01HG002585 (G.Wa., M.St.), Gordon and Betty Moore Foundation
GBMF 4559 (G.Wa., M.St.), 1K99HG009916-01 (S.E.C.), R01HG006855 (Se.Ka., R.E.H.), BIO2015-70777-P,
Ministerio de Economia y Competitividad and FEDER funds (M.M-A., V.W., R.G., D.G-M.), NIH CTSA grant
UL1TR002550-01 (P.M.), Marie-Skłodowska Curie fellowship H2020 Grant 706636 (S.K-H.), R35HG010718
(E.R.G.), FPU15/03635, Ministerio de Educación, Cultura y Deporte (M.M-A.), R01MH109905, 1R01HG010480
(A.Ba.), Searle Scholar Program (A.Ba.), R01HG008150 (S.B.M.), 5T32HG000044-22, NHGRI Institutional
Training Grant in Genome Science (N.R.G.), EU IMI program (UE7-DIRECT-115317-1) (E.T.D., A.V.), FNS funded
project RNA1 (31003A_149984 ) (E.T.D., A.V.), DK110919 (F.H.), F32HG009987 (F.H.)
Conflicts of interest
F.A. is an inventor on a patent application related to TensorQTL; S.E.C. is a co-founder, chief technology officer and
stock owner at Variant Bio; E.R.G. is on the Editorial Board of Circulation Research, and does consulting for the City
of Hope / Beckman Research Institut; E.T.D. is chairman and member of the board of Hybridstat LTD.; B.E.E. is on
the scientific advisory boards of Celsius Therapeutics and Freenome; G.G. receives research funds from IBM and
Pharmacyclics, and is an inventor on patent applications related to MuTect, ABSOLUTE, MutSig, POLYSOLVER
and TensorQTL; S.B.M. is on the scientific advisory board of Prime Genomics Inc.; D.G.M. is a co-founder with
.CC-BY 4.0 International licenseIt is made available under a
was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which. http://dx.doi.org/10.1101/787903doi: bioRxiv preprint first posted online Oct. 3, 2019;
equity in Goldfinch Bio, and has received research support from AbbVie, Astellas, Biogen, BioMarin, Eisai, Merck,
Pfizer, and Sanofi-Genzyme; H.K.I. has received speaker honoraria from GSK and AbbVie.; T.L. is a scientific
advisory board member of Variant Bio with equity and Goldfinch Bio. P.F. is member of the scientific advisory boards
of Fabric Genomics, Inc., and Eagle Genomes, Ltd. P.G.F. is a partner of Bioinf2Bio.
Affiliations
1. The Broad Institute of MIT and Harvard, Cambridge, MA, USA
2. Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
3. Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
4. Population Health and Genomics, University of Dundee, Dundee, Scotland, UK
5. New York Genome Center, New York, NY, USA
6. Department of Systems Biology, Columbia University, New York, NY, USA
7. Department of Computer Science, Princeton University, Princeton, NJ, USA
8. Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
9. Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
10. Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
11. Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
12. Department of Pathology, Stanford University, Stanford, CA, USA
13. Data Science Institute, Vanderbilt University, Nashville, TN, USA
14. Clare Hall, University of Cambridge, Cambridge, UK
15. MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
16. Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN,
USA
17. Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
18. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
19. Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
20. Scripps Research Translational Institute, La Jolla, CA, USA
21. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA,
USA
22. Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia,
Spain
23. Department of Statistics and Operations Research, Universitat Politècnica de Catalunya (UPC), Barcelona,
Catalonia, Spain
24. Department of Genetics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
25. Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman
School of Medicine, Philadelphia, PA, USA
26. Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
27. Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
28. Swiss Institute of Bioinformatics, Geneva, Switzerland
29. Department of Genetics, Stanford University, Stanford, CA, USA
30. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
31. Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
32. Department of Genetics, Harvard Medical School, Boston, MA, USA
33. Program in Medical and Population Genetics, The Broad Institute of Massachusetts Institute of Technology and
Harvard University, Cambridge, MA, USA
34. Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
35. Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
.CC-BY 4.0 International licenseIt is made available under a
was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which. http://dx.doi.org/10.1101/787903doi: bioRxiv preprint first posted online Oct. 3, 2019;
36. Department of Human Genetics, University of Chicago, Chicago, IL, USA
37. Center for Genetic Medicine, Department of Pharmacology, Northwestern University, Feinberg School of
Medicine, Chicago, IL, USA
38. Department of Twin Research and Genetic Epidemiology, King’s College London, London, UK
39. Department of Statistics, University of Chicago, Chicago, IL, USA
40. Department of Biomathematics, University of California, Los Angeles, Los Angeles, CA, USA
41. Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
42. Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
43. Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
44. Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, CA, USA
45. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA,
USA
46. Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
47. Department of Statistics and Operations Research and Department of Biostatistics, University of North Carolina,
Chapel Hill, NC, USA
48. Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona. Spain.
49. Departments of Biomedical Data Science and Statistics, Stanford University, Stanford, CA, USA
50. Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago,
Chicago, IL, USA
51. Bioinformatics Research Center and Departments of Statistics and Biological Sciences, North Carolina State
University, Raleigh, NC, USA
52. Department of Computer Sciences, Faculty of Sciences, University of Porto, Porto, Portugal
53. Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
54. Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
55. Columbia University Mailman School of Public Health, New York, NY, USA
56. Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
57. Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
58. National Institute for Biotechnology in the Negev, Beer-Sheva, Israel
59. Leidos Biomedical, Frederick, MD, USA
60. Leidos Biomedical, Rockville, MD, USA
61. UNYTS, Buffalo, NY, USA
62. Washington Regional Transplant Community, Annandale, VA, USA
63. Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
64. Gift of Life Donor Program, Philadelphia, PA, USA
65. LifeGift, Houston, TX, USA
66. Center for Organ Recovery and Education, Pittsburgh, PA, USA
67. LifeNet Health, Virginia Beach, VA. USA
68. National Disease Research Interchange, Philadelphia, PA, USA
69. Van Andel Research Institute, Grand Rapids, MI, USA
70. Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
71. Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer
Institute, Bethesda, MD, USA
72. Temple University, Philadelphia, PA, USA
73. Virgina Commonwealth University, Richmond, VA, USA
74. European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
75. Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
76. Carl Icahn Laboratory, Princeton University, Princeton, NJ, USA
77. Department of Population Health Sciences, The University of Utah, Salt Lake City, Utah, USA
.CC-BY 4.0 International licenseIt is made available under a
was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which. http://dx.doi.org/10.1101/787903doi: bioRxiv preprint first posted online Oct. 3, 2019;
78. Departments of Medicine, Biomedical Engineering, and Mental Health, Johns Hopkins University, Baltimore,
MD, USA
79. Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
80. Department of Medical Biology, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria,
Australia
81. Altius Institute for Biomedical Sciences, Seattle, WA, USA
82. Division of Genetics, University of Washington, Seattle, WA, University of Washington, Seattle, WA, USA
83. Department of Cardiology, University of Washington, Seattle, WA, USA
84. HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
85. Genome Sciences, University of Washington, Seattle, WA, USA
86. National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
87. Division of Neuroscience and Basic Behavioral Science, National Institute of Mental Health, National Institutes
of Health, Bethesda, MD, USA
88. National Institute on Drug Abuse, Bethesda, MD, USA
89. Office of Strategic Coordination, Division of Program Coordination, Planning and Strategic Initiatives, Office of
the Director, National Institutes of Health, Rockville, MD, USA
90. Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
.CC-BY 4.0 International licenseIt is made available under a
was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
The copyright holder for this preprint (which. http://dx.doi.org/10.1101/787903doi: bioRxiv preprint first posted online Oct. 3, 2019;
