Supplementary information Methods Seed search Below we outline very formally the procedure used to detect the conserved complementary boxes in a set of orthologous sequences. While some readers might find the set-theoretic notation cumbersome, we believe that it gives the most concise and short description of the method. Denote by S the set of species. For each species s ∈ S denote by W (s) the set of sequence windows to be searched in that specie. Each sequence window w ∈ W (s) is a neighborhood of a splice site extending le nucleotides in the exonic part and li nucleotides in the intronic part of the sequence. By default, li = 150 and le = 0 were used. As explained in the previous section, splice sites were matched across species by the relation of orthology. Denote by G the set of classes of orthologous splice sites and consider the mapping f which appoints to each sequence window w ∈ W (s) the class f(w) ∈ G of splice sites, which it surrounds. An element of G will be also called splice site, without any reference to species. Let Ω = {A, C, G, T } be the nucleotide alphabet and Ωn be the set of n- mers on Ω (by default n = 9). When it does not lead to a confusion, we treat w ∈ W (s) both as a nucleotide sequence and as a collection of its n-mer n subsequences. We define the relation Rs on the Cartesian product Ω × G such that for each species s ∈ S, for each sequence window w ∈ W (s), and for each n-mer x ∈ w, the value of Rs(x, g) is defined true if g = f(w). In other words, Rs(x, g) is defined true if the n-mer x occurs in a sequence window of the splice site g in the species s. Technically, Rs is implemented as a hash table, which appoints to each n-mer the (indexed) list of g ∈ G, in which it occurs. Note that Rs is a very useful object; for instance, the intersection ∩s∈SRs(·, g) gives the list of all conserved n-mers for each g. ∗ ∗ ∗ Similarly, the relation Rs(x , g) is defined true if g = f(w), where x is the ∗ ∗ reverse complement of x. That is, Rs(x , g) is true if the reverse complement of the n-mer x occurs in a sequence window surrounding the splice site g in the species s. More generally, one can treat x∗ as the list of all n-mers that can base-pair with x. If Wobble pairings are not allowed then x∗ consists only of one element, which is the exact reverse complement to x, but it would contain more than one element when GT base-pairs are allowed. In the latter case, the relation ∗ ∗ ∗ Rs(x , g), is defined true for all elements of the list x . The upper limit of ∗ ∗ nGT, of GT base-pairs prevents x (and the hash table Rs) from growing too quickly. Additionally, the lower limit of nGC,min of G or C nucleotides reduces the number of AT-rich n-mers. By default, nGT,max = 1 and nGC,min = 2 were used. The next step is to obtain candidate complementary sequences by intersect- ∗ ∗ ing Rs and Rs. However, when intersecting Rs and Rs, we need to know which sequence windows are to be matched with each other. This piece of information comes separately, in the form of a binary relation relevant to the questions we ask about splicing. Consider, for instance, the binary relation I on G×G which is true for all pairs (d, a), where d and a are the ends of an annotated intron. Then, in order to detect complementary seeds at the ends of annotated introns, ∗ we need to find x such that Rs(x, d) and Rs(x, a) are both true for some true

1 I(d, a). That is, we are looking for the set

∗ Cs(I) = {x | ∃g1, g2 : Rs(x, g1)& Rs(x, g2)& I(g1, g2)}.

The set Cs(I) has been studied extensively in [17]. Another example is the identity relation id, i.e., id(g1, g2) is true if and only if g1 = g2. Then the set Cs(id) consists of all n-mers that contain a complementary n-mer in the same sequence window; these are local cis-structures with boxes forming hairpin structures. The set Cs(A), for some relation A, can be interpreted as a set of all possi- ble secondary structures in the species s, which are stable enough according to the constraints imposed by n, nGT,max, and nGC,min. In other words, this set contains information on all long enough complementary stretches of nucleotides. However, not all genome-wide combinations of boxes are needed, so the relation A comes as an input defining the “matching pattern”. Obviously, the compu- tation of Cs(A) and, therefore, the performance of the entire method critically depend on A. In what follows next, we consider only the relation A(g1, g2) which is defined true if and only if g1 and g2 are splice sites taken from the same . The relations I and id defined earlier are subsets of A. Next, hav- ing computed the set Cs(A), we want to compute the intersection ∩s∈SCs to obtain the conserved complementary n-mers. However, in order to account for evolutionary changes and the lack of alignment in some species, we used the following procedure called soft intersection. n Given two n-mer sequences x1, x2 ∈ Ω , we define the distance d(x1, x2) to be the number of mismatches between x1 and x2 (Hamming distance). If n x ∈ Ω and w ∈ W (s), we define d(x, w) = miny∈w d(x, y) (distance from a point to a line). We say that the n-mer x ∈ Cs(A) is ε-conserved in the species s0 if d(x, w0) ≤ ε for the orthologous window w0 ∈ W (s0). We next discard the n-mer from Cs(A) unless it is ε-conserved in at least m species. By default ε = 3 and m = 9 (for 12 species considered). After this procedure, each n-mer in Cs(A) has a relative n-mer in sufficiently many species and is considered as conserved. The list of conserved n-mers is reported after short refinement described below. The seed search reports only the list of conserved complementary n-mers along with their locations at splice sites. The task of combining seeds into a secondary structure per se is a very complex problem which falls outside of the scope of this research. However, we still do a few extra steps after the seed search to obtain visually tractable results. First, some structures may contain adjacent or overlapping complementary boxes. If, for instance, box A is complementary to box B and these two boxes overlap then the entire secondary structure is discarded as non-existent. If box A is complementary to box B, box A’ is complementary to box B’, box A overlaps with box A’, and box B overlaps with box B’, then box A and box A’ are merged and box B and box B’ are merged (extension). Next, the nucleotide sequences of windows surrounding splice sites are split by boxes and aligned separately by MUSCLE [37] and then joined as was explained in [17].

Controls The control procedure (re-wiring) for trans-structures was organized as a series of steps, in which the sequence windows surrounding splice sites drawn on - dom from different were exchanged. At each step, two elements, g1 and g2, were selected randomly from the set G with the condition that (i) g1 and g2

2 were both donor splice sites or both acceptor splice sites and (ii) g1 and g2 were drawn from different genes, and the respective permutation was applied to the ˜ ˜ mapping f yielding the new mapping f such that f(w) = g2 when f(w) = g1 ˜ ˜ and f(w) = g1 when f(w) = g2. In the next step, f replaced f. This operation, ∗ in fact, only concerns the hash tables Rs and Rs, not the original sequences, from which they were created. This allows for fast and efficient re-hashing of ∗ Rs and Rs according to repetitive permutations of the mapping f. The per- mutations were repeated roughly one million times, so that, on average, each splice site was permuted at least twice. The additional requirement of preserv- ing the GC content was implemented by creating ten GC-content bins, from 0% to 100%, and exchanging only splice sites corresponding to the same bin. The degree of conservation was accounted in a similar way, by exchanging only splice sites which belong to the same conservation rate bins. The rate of conser- vation itself was inferred from the pairwise fractional identity between species as in [17] by using the k-mer distance[36] without any use of multiple sequence alignments. In each case, the entire control procedure was repeated N = 20 times to construct interval estimates for the rate of false positive predictions. The efficacy of the re-wiring procedure was assessed by using the re-wiring factor, which is defined for each gene to be the proportion of sequence windows that were replaced during re-wiring by windows taken from different genes. As expected, the re-wiring factor decreased with increasing control constraints so that, on average, 94% of splice sites were re-wired with the GC-content constraint, 89% were re-wired with the conservation constraint, and 87% were re-wired with both constraints. The control procedure for cis-structures was implemented as follows. Firstly, we produced multiple sequence alignments for each g ∈ G, shuffled randomly the columns of these alignments, computed the matrix of dinucleotide frequencies for the original and the shuffled alignment, and calculated the distance factor, by which the two matrices differ from each other. The distance factor was defined as Euclidean distance in the 16-dimensional space of 4×4-matrices. Next, all g ∈ G were appointed to 25 bins uniformly covering the range (from 0 to 4) of values of the distance factor, and the proportion of splices sites with cis- structures was computed for each bin. The interval estimate for the number of cis-structures when the distance factor is zero was computed from the intercept of the linear model by using distance factor as a predictor.

P-value of a box pair As in [17], we scored each pair of boxes by computing an individual p-value, which was defined as a probability of observing two complementary w-long words in n random sequences (w = 9, n varies from 7 to 12). Importantly, the probability p1 of observing two complementary words in one sequence is context-dependent, e.g., CpG-rich sequences are more likely to contain a pair of complementary words than sequences with uniform nucleotide distribution. This probability was estimated from the first-order Markov model inferred from the local nucleotide context of the intron with an addition of small number of pseudo-counts that reflect the average nucleotide composition across the gene. The value of p1 was computed by the formula X p = (L − w + 1)2 f f a1 f a2 . . . f aw−1 f˜aw ... f˜a3 f˜a2 f˜a1 , 1 a1 a2 a3 aw aw−1 a2 a1 a1,...,aw

3 a ˜b where L is the length of the sequence, fb and fa are the Markov transition probabilities for the original sequence and its reverse complement, respectively, ˜b and fa and f are the corresponding marginal distributions. Next, given that one sequence contains complementary words, the conditional probability p2 of observing two complementary words in another sequence depends on the degree of similarity between sequences: in an extreme case of 100% identity, it is not surprising at all to find a pair of complementary words in one sequence given that another sequence contains such a pair. Accordingly, the value of p2 was estimated as (α2 + (1 − α)2/3)w−1, where α is the pair-wise fractional identity between species; the latter is derived from the local nucleotide context using n−1 the k-mer distance [36]. The resulting p-value was p1p2 . In order to account for multiple simultaneous tests, we used Bernoulli-type of correction of the form p∗ = 1 − (1 − p)m, where p∗ is the corrected p-value and m is the number of independent tests.

Supplementary Tables and Figures Supplementary Table 1. The complete list of predicted box pairs (by gene name). Search parameters were: le = 0, li = 150, n = 9, nmax(GT ) = 1, nmin(GC) = 2, ε = 3, smin = 9. The columns are (left to right): ’No.’ is the ordinal number (a Genome Browser window will open if the hyperlink is pressed); ’Name’ is the gene mane; ’Gene description’ is the hg19 annotation of the gene; ’Arr’ is the code abbreviation of the box pair arrangement (see Results); ’Comment’ contains cis/trans for DD and AA arrangements and in- tron/exon for DA and AD arrangements in case of RefSeq-annotated splicing events; ’Alt’ contains check mark if the splice site (for DD or AA) or the intron (for DA) or the exon (for AD) is alternative according to RefSeq-annotation; ’Chr’ is the name of the and strand; 5’-SS and 3’-SS are the coor- dinates of the 5’-splice site and the 3’-splice site, respectively; ∆ is the distance between 5’-and 3’-splice sites; 5’-box and 3’-box are the sequences of the 5’- box and the 3’-box, respectively; ’L’ is the length of the boxes; ’|E|’ is the absolute value of the equilibrium free energy; HCMCBFECLOOA is the first letter of each of the species listed in the following order: H. sapiens, C. jacchus, M. musculus, C. familiaris, B. taurus, F. catus, E. caballus, C. porcellus, L. africana, O. cuniculus, O. anatinus, A. carolinensis, where bullets denote that a structure was found, open circles denote that an orthologous intron, but not structure, was found, and an empty space indicated that no orthologous intron was found; P-values are reported after the correction for multiple hypothesis testing (see Methods). Supplementary Table 2. The complete list of predicted box pairs (by gene name). Search parameters were: le = 0, li = 150, n = 10, nmax(GT ) = 1, nmin(GC) = 2, ε = 3, smin = 9. The rest of the legend of the same as in Supplementary Table 1. Note that the total number of tests in the correction for multiple hypothesis testing is smaller than that in Supplementary Table 1, and the P-values are more significant than those in Supplementary Table 1.

4 Supplementary Table 1: 9-nt seed search

No Name Gene description Arr Annot Alt Chr 5’-SS 3’-SS ∆ 5’-box 3’-box L |E| HCMCBFECLOOA P-value 1 AASS Alpha-aminoadipic semialdehyde synthase, AD 7− 121773795 121753171 20624 GAGACCAGA TCTGGTCTT 9 17.9 •••••••••• 1.6·10−22 2 ABHD14A N/A DD trans 3+ 52019287 52020520 1233 TGGCTATGT GCATAGCCA 9 17.9 •••••••••• ◦ 4.8·10−22 −14 3 ABI1 Abl interactor 1 isoform d DA intron X 10− 27044583 27040712 3871 TAGCATGCAT GTGCATGCTG 10 18.7 •••••••••• 4.4·10 4 ACADVL Very long-chain specific acyl-CoA dehydrogenase, DD cis 17+ 7126556 7126556 0 CCTGGGGCA TGCCCTAGG 9 20.6 • • • • • • • • • ◦ 6.1·10−8 5 ACIN1 Apoptotic chromatin condensation inducer in the DA 14− 23559190 23535217 23973 GGGGGGAGG CCTTCCCCC 9 21.4 •••••••••• 7.0·10−11 −6 6 ACIN1 Apoptotic chromatin condensation inducer in the DA intron X 14− 23540635 23540395 240 CCACCACCTCC GGAGGTGGTGG 11 26.3 ••••••••• 3.8·10 7 ACIN1 Apoptotic chromatin condensation inducer in the AD 14− 23559310 23533563 25747 CCTGCCCCG CGGGGCAGG 9 23.2 • • • • • • • ◦ • • 3.7·10−11 8 ACIN1 Apoptotic chromatin condensation inducer in the AD 14− 23538826 23533563 5263 CTCTCTTCCC GGGAAGGGAG 10 20.1 •••••••••• 9.0·10−13 9 ACSL6 Long-chain-fatty-acid–CoA 6 isoform a AD 5− 131325857 131310450 15407 CCTCTCTGA TCAGGGAGG 9 18 • • • • • • • • • ◦ 1.8·10−20 −4 10 ADAM22 Disintegrin and metalloproteinase AD exon X 7+ 87808249 87808357 108 TGAAATGTTT GAACATTTCA 10 13.9 •••••••••• 5.2·10 11 ADAMTS6 A disintegrin and metalloproteinase with AD exon 5− 64510759 64510620 139 TGTTTTCAAT ATTGGAAACA 10 13 • • • • • • • ◦ • • 3.2·10−12 12 ADAMTS6 A disintegrin and metalloproteinase with AD exon 5− 64558789 64558643 146 CTGTGTTTT AAGACACAG 9 13.5 ••••••◦•••◦ 1.3·10−14 13 ADAMTSL1 ADAMTS-like 1 isoform 4 precursor DD trans 9+ 18675905 18721663 45758 CTGATGTTA TAGCATCAG 9 14.2 • • • • • • • • • ◦ 4.5·10−20 14 AFF2 AF4/FMR2 family member 2 isoform 5 AA cis X+ 148062267 148062267 0 CATCTGTTT AAATAGATG 9 11.9 •••••••••• ◦ 3.3·10−6 15 AFF2 AF4/FMR2 family member 2 isoform 5 AA trans X+ 147743428 148062267 318839 CATCTGTTT AAATAGATG 9 11.9 • • • • ◦ • • • • • 1.8·10−9 16 AFTPH Aftiphilin isoform c DD trans 2+ 64806680 64808407 1727 CTCTGCTGAT GTCAGCAGAG 10 20.1 •••••••••◦ • 1.0·10−9 −5 17 AFTPH Aftiphilin isoform c DA intron X 2+ 64806680 64808323 1643 GAAATTCAG CTGAATTTC 9 12.8 ••◦•••••◦• • 6.1·10 18 AFTPH Aftiphilin isoform c DD cis 2+ 64806680 64806680 0 GTTCAGACA TGTTTGAAC 9 13.8 ••••••••••• 2.7·10−4 19 AGPAT1 1-acyl-sn-glycerol-3-phosphate acyltransferase DD trans 6− 3491318 3486441 4877 GAAGGGGAG TTCCCCTTC 9 18.3 • • • • • • • • • ◦ 1.5·10−22 20 AKAP6 A- anchor protein 6 DD cis 14+ 33069998 33069998 0 AAGTTTGCC GGTAAACTT 9 13.8 ••••• ••◦••◦ 5.2·10−9 21 AKAP9 A-kinase anchor protein 9 isoform 2 AA cis 7+ 91671359 91671359 0 CTTTTAACCCC GGGGTTAAAAG 11 19.1 ••••••••◦• ◦ 4.6·10−13 5 22 ALOXE3 Epidermis-type lipoxygenase 3 isoform 1 DD trans 17− 8021161 8017801 3360 GGGCAGGGG TCCCTGCCC 9 22.3 • • • • • • • • • ◦ 2.2·10−24 23 AMBRA1 Activating molecule in BECN1-regulated autophagy AA cis 11− 46534363 46534363 0 CAGGGATTA TAATCTCTG 9 13.5 •••••◦••••◦◦ 2.6·10−15 −17 24 ANK2 -2 isoform 2 AD exon X 4+ 114244914 114244950 36 CTAAAGTATC GATGCTTTAG 10 14.3 • • • • • • • • • ◦ 1.1·10 25 ANK2 Ankyrin-2 isoform 2 AA trans 4+ 114244914 114254209 9295 TCTGTTGCA TGCAACAGA 9 17.3 • ◦ • • • • • • • • 5.3·10−19 26 ANK3 Ankyrin-3 isoform 2 DA 10− 61840294 61819188 21106 GAGACATTTT GAAATGTCTT 10 14.3 ••◦◦•••••••◦ 1.4·10−18 27 ANK3 Ankyrin-3 isoform 2 AD 10− 61894131 61828394 65737 CATGCATTA TAGTGCATG 9 14.1 ••◦•••••••• 2.6·10−13 −9 28 ANK3 Ankyrin-3 isoform 2 DD cis X 10− 61828394 61828394 0 AGGCAGTCA TGATTGCCT 9 17.4 ••◦••••••◦•◦ 6.2·10 29 ANK3 Ankyrin-3 isoform 2 AA trans 10− 61865817 61836206 29611 CTTTGAAAT ATTTCAAAG 9 11.3 ••◦•••••••◦◦ 6.5·10−12 30 ANK3 Ankyrin-3 isoform 2 AA cis 10− 61819188 61819188 0 TTGAGGACATT AATGTCTTCAA 11 16.8 •••••••••••• 9.7·10−8 31 ANKRD13B Ankyrin repeat domain-containing protein 13B AD 17+ 27936103 27939024 2921 CCGCAGCTT AAGCTGTGG 9 17.8 • • ◦ • • • • • • • 7.5·10−14 32 ANKRD52 Serine/-protein phosphatase 6 DD trans 12− 56651066 56647505 3561 GGGGAGGAG CTCCTCCCC 9 22.2 •••••••••• 8.6·10−20 33 ANXA6 Annexin A6 isoform 2 DA 5− 150513987 150490205 23782 GGGGAGAGG CCTCTCTCC 9 19.2 • • • • • • • • ◦ • 2.2·10−19 34 AP1S1 AP-1 complex subunit sigma-1A DD trans 7+ 100797798 100802477 4679 AGGGGAGGGGG CTCCCTCCCCT 11 26.7 •••••••••• 8.4·10−16 35 AP2A1 AP-2 complex subunit alpha-1 isoform 2 DA 19+ 50305146 50305790 644 GCGGGCAGC GCTGCCTGC 9 21.2 • • • • • • • • • ◦ 9.7·10−18 36 APBB1 Amyloid beta A4 precursor protein-binding family DA 11− 6424548 6422302 2246 AAGAGGAGG CCTTCTCTT 9 15.7 ••••••••• 4.0·10−17 37 ARAF Serine/threonine--Raf AA trans X+ 47424383 47426282 1899 CTGACCATG TATGGTCAG 9 16.3 • • • • • • • • • ◦ 7.1·10−21 38 ARAP1 Arf-GAP with Rho-GAP domain, ANK repeat and PH DD trans 11− 72406762 72403797 2965 CCCAGGTGG CCACCTGGG 9 21.7 ••••◦•••••◦ 3.3·10−21 39 ARHGAP15 Rho GTPase-activating protein 15 AA trans 2+ 144276834 144381701 104867 TAATGAAGC GTTTCATTA 9 11.8 •••••••••• 1.6·10−6 40 ARHGEF2 Rho guanine nucleotide exchange factor 2 isoform AD exon 1− 155936678 155936610 68 ACCCTCTCT GGAGAGGGT 9 19.9 • • • • • • • • • ◦ 5.8·10−16 41 ARID1A AT-rich interactive domain-containing protein 1A AA trans 1+ 27099302 27100070 768 CTCACTCTG CAGAGTGAG 9 17.5 ••••◦•••••◦◦ 2.6·10−28 42 ARID5B AT-rich interactive domain-containing protein DD trans 10+ 63819054 63845659 26605 AGCAACTTA TGAGTTGCT 9 15.1 ••••◦•••••◦◦ 7.3·10−27 43 ARMC8 Armadillo repeat-containing protein 8 isoform 3 AD 3+ 137942477 137964025 21548 TCCCTGCCT AGGCAGGGA 9 22 ••◦••••••• ◦ 1.8·10−14 44 ARNT Aryl hydrocarbon receptor nuclear translocator AD 1− 150814944 150785647 29297 TTTTCTCTCT GGAGAGAAAG 10 15.9 ••••••••••◦◦ 1.2·10−27 45 ARR3 -C AD X+ 69489511 69489753 242 TCTTTTTCT AGAAAAGGA 9 12.3 •••••••◦•• ◦ 8.8·10−24 Supplementary Table 1: (continued)

46 ASAP3 Arf-GAP with SH3 domain, ANK repeat and PH DD trans 1− 23767879 23761025 6854 GGGAGAGAA TTCTCTTCC 9 16 •••◦•••••• ◦ 1.7·10−24 47 ASXL3 Putative Polycomb group protein ASXL3 AA trans 18+ 31241579 31251710 10131 TCATTATCT AGATAATGA 9 13.4 ••••◦•••••◦◦ 1.8·10−19 48 ATF6B Cyclic AMP-dependent ATF-6 DA 6− 32095902 32083745 12157 GGGGAGGGG CTCCTCCCC 9 21.3 ••••••••• 2.4·10−15 49 ATG4A Cysteine protease ATG4A isoform a DD trans X+ 107381114 107381221 107 CTGCTGCTCA TGAGCAGCAG 10 21.8 ••••••••• 9.0·10−9 50 ATG9A Autophagy-related protein 9A DA 2− 220088827 220086889 1938 CATGGTGTT AGCACCATG 9 16 ••◦•••••••◦ 3.6·10−21 51 ATG9B Autophagy-related protein 9B AD exon 7− 150711000 150710817 183 GCCCGCCCC GGGGTGGGC 9 23.8 ••◦••••••• ◦ 4.7·10−26 52 ATP2A2 Sarcoplasmic/ calcium DD trans 12+ 110783923 110784126 203 CCAGATCAC GTGATCTGG 9 17.7 •••••••••◦◦◦ 4.5·10−22 53 ATP2B1 Plasma membrane calcium-transporting ATPase 1 AD 12− 90021493 89992366 29127 GGAAAGCTTTA TAAAGCTTTCT 11 17 •••••••••◦ • 4.0·10−11 54 ATP2B4 Plasma membrane calcium-transporting ATPase 4 AD 1+ 203671171 203702528 31357 CTTTCTTGT ACAAGAGAG 9 13.7 • • • • • • • ◦ • • 2.2·10−15 55 ATP2C1 Calcium-transporting ATPase type 2C member 1 DD trans 3+ 130675023 130720158 45135 AAGAGAAGA TCTTTTCTT 9 12.7 ••◦•••••••◦◦ 9.4·10−23 56 ATXN2L Ataxin-2-like protein isoform E DD trans 16+ 28847443 28847497 54 GTGGGGCAG CTGTCCCAC 9 19.1 • • ◦ • • • • • • • 9.5·10−1 57 ATXN2L Ataxin-2-like protein isoform E DA 16+ 28847497 28848048 551 GGCTGTCCC GGGACAGCT 9 20.9 • • • • • ◦ • • • • 3.2·10−7 58 ATXN7L1 Ataxin-7-like protein 1 isoform 3 DD cis 7− 105279933 105279933 0 ATTTCTCTT AAGGGAAAT 9 11.9 •••••••••• ◦ 1.5·10−2 59 AUTS2 Autism susceptibility gene 2 protein isoform 3 AA trans 7+ 69599521 70240342 640821 AGATGACAA TTGTCATTT 9 12.7 • • ◦ • • • • • • • 5.3·10−4 60 BAI2 Brain-specific angiogenesis inhibitor 2 DA 1− 32200783 32197020 3763 GGGGTGGGT ACTCACCCC 9 20 ••••••••• 9.7·10−15 61 BAI2 Brain-specific angiogenesis inhibitor 2 AD 1− 32209958 32196400 13558 GCTGTCCCT GGGGACAGC 9 20.9 ••••••••◦• ◦ 9.7·10−24 62 BAI2 Brain-specific angiogenesis inhibitor 2 DA 1− 32207400 32205635 1765 TGGAAGAAG CTTCTTCCA 9 16.2 • • ◦ • • • • • • • 4.9·10−16 63 BAT2L2 Protein BAT2-like 2 DD trans 1+ 171540560 171553665 13105 TGAGGAAAT ATTTCCTCA 9 15.2 • • ◦ • • • • • • • 1.5·10−17 64 BAT3 Large proline-rich protein BAT3 isoform b AD exon 6− 31616741 31616687 54 CTTCTCCCAGA TCTGGGAGAAG 11 23.1 •••••••••• 9.4·10−17 65 BAT3 Large proline-rich protein BAT3 isoform b AD 6− 31619553 31612301 7252 GGGGCAGGGA TCCCTGCCCC 10 26.5 • • ◦ • • • • • • • 1.5·10−16 66 BCOR BCL-6 corepressor isoform c AA trans X− 39930943 39923103 7840 AGTTATCTAA TTAGATGACT 10 14.4 ••••••••◦• ◦ 1.7·10−7 67 BIRC3 Baculoviral IAP repeat-containing protein 3 DA intron 11+ 102192631 102195191 2560 GTTTTGTGCAT ATGCACAAAAC 11 17.9 ••••••••• 4.4·10−17

6 X −10 68 BMP1 N/A AA cis X 8+ 22034473 22034473 0 CCAGCTCGG CTGAGCTGG 9 18.9 •••••••••• ◦ 1.3·10 69 BRD2 Bromodomain-containing protein 2 DA intron 6+ 32942542 32943160 618 GCTGCGGCCCC GGGGCCGCAGT 11 29.1 • • • • • • • • • ◦ 1.3·10−22 70 BZRAP1 Peripheral-type benzodiazepine DA 17− 56403653 56397942 5711 AGAGGGGAG CTTCCCTCT 9 18.1 •••••••••• 8.0·10−21 71 C10orf107 Hypothetical protein LOC219621 DA 10+ 63450379 63525696 75317 TGCTTAAAG CTTTAGGCA 9 13.4 •••••••••◦◦ 7.7·10−12 72 C10orf11 Leucine-rich repeat-containing protein C10orf11 DA intron 10+ 77542780 77795765 252985 TCTGTCAGCA TGCTGACAGG 10 20 ••••••••• 8.8·10−1 73 C11orf30 Protein EMSY AA trans 11+ 76246938 76256840 9902 AAGAGAAAC GTTTCTTTT 9 11.3 •••••••••• 8.2·10−12 74 C11orf30 Protein EMSY DD cis 11+ 76250684 76250684 0 GTGCATCCATT AATGGATGCGC 11 20.3 •••••••••• 1.1·10−4 75 C11orf30 Protein EMSY DD trans 11+ 76247103 76255866 8763 GTTTTCTCT AGAGGAAAC 9 13.4 ••◦•••••••◦◦ 1.4·10−23 76 C12orf41 Hypothetical protein LOC54934 AD exon 12− 49072933 49072818 115 GTGGAGTTA TAACTCCAC 9 16.5 ••••••••◦•◦◦ 1.1·10−25 77 C12orf64 open reading frame 64 AA cis 12+ 80605728 80605728 0 GAGGAAAACA TGTTTTCTTC 10 14.5 ••••••••••◦◦ 3.9·10−6 78 C15orf41 Hypothetical protein LOC84529 isoform 2 DD trans 15+ 36936524 36984376 47852 TTTGTGAGG CTTCACAAA 9 13.3 • • • • • • • • • ◦ 1.7·10−6 79 C15orf41 Hypothetical protein LOC84529 isoform 2 AD 15+ 36936478 36983965 47487 CAGTAATTA TAATTACTG 9 11.9 • • ◦ • • • • • • • 1.5·10−5 80 C15orf41 Hypothetical protein LOC84529 isoform 2 AA cis 15+ 36936478 36936478 0 CTGGAACAA TTGTTCCAG 9 16 •••••••••• 9.9·10−1 81 C15orf41 Hypothetical protein LOC84529 isoform 2 DD cis 15+ 36984376 36984376 0 GAGATGTGT ACACATTTC 9 14 ••••◦•••••◦◦ 1.9·10−6 82 C17orf49 MLL1/MLL complex subunit C17orf49 isoform 1 DA intron 17+ 6918197 6918380 183 GGGGTGGGGC GCCCCGCCCC 10 27.1 •••••••••• 2.4·10−4 83 C19orf43 Hypothetical protein LOC79002 AA cis 19− 12842235 12842235 0 GGAGCTGGG CCCGGCTCC 9 21.3 •••••◦••••◦◦ 2.2·10−8 84 C2orf34 Hypothetical protein LOC79823 AD exon 2+ 44933425 44933480 55 TCTCTCTGA TCAGAGGGA 9 17.1 ••••••••••• 2.1·10−5 85 C2orf34 Hypothetical protein LOC79823 DD cis 2+ 44993700 44993700 0 ACTTTAATC GATTAAAGT 9 11.8 ••••◦◦•••• • 7.7·10−5 86 C5orf36 Hypothetical protein LOC285600 isoform 1 AA trans 5− 93805816 93775826 29990 GGCCTTAAA TTTAAGGCT 9 14.9 ••••◦••••••• 3.0·10−10 87 C6orf174 Hypothetical protein LOC9729 DD cis 6− 127771134 127771134 0 CTCTTGAAG TTTCAAGAG 9 13.5 • • • • • ◦ • • • • 6.7·10−9 88 C9orf25 Hypothetical protein LOC203259 isoform 6 DD trans 9− 34458234 34402702 55532 GGAGGGAGGGAA TTCCCTCCCTCC 12 28.8 ••••••••• 7.1·10−13 89 C9orf93 Hypothetical protein LOC203238 DD trans 9+ 15846845 15874661 27816 ACAGTGTTA TAACATTGT 9 12.8 • • ◦ • • • • • • • 1.4·10−6 90 C9orf93 Hypothetical protein LOC203238 AD exon 9+ 15846699 15846845 146 TGTTTTCTG TAGAAAACA 9 12.5 •••••••••• 1.0·10−5 91 CACNA1C Voltage-dependent L-type calcium channel subunit AA trans 12+ 2691987 2743462 51475 GGGGCAGGG CTCTGCCCC 9 21.1 ••◦••••••• ◦ 8.0·10−16 Supplementary Table 1: (continued)

92 CACNA1C Voltage-dependent L-type calcium channel subunit AD 12+ 2743462 2774874 31412 TTTTCCTCT AGAGGGAAA 9 14.5 ••◦••••••• ◦ 6.4·10−22 93 CACNA1C Voltage-dependent L-type calcium channel subunit AA trans 12+ 2614007 2693668 79661 TCCGTTCTT AAGAATGGA 9 14.8 ••••◦••••• ◦ 6.7·10−22 94 CACNA1C Voltage-dependent L-type calcium channel subunit AD 12+ 2691987 2742878 50891 AGGGCAGGG CTCTGCCCT 9 19.9 ••••◦••••• ◦ 8.2·10−17 95 CACNA1C Voltage-dependent L-type calcium channel subunit AA trans 12+ 2613601 2691987 78386 CTTCTTTCCT GGGAAAGAAG 10 17.1 ••••◦••••• • 3.0·10−24 96 CACNA1C Voltage-dependent L-type calcium channel subunit AA trans 12+ 2743462 2783649 40187 TTCTTCTTC GAAGAGGAA 9 13.8 ••••••••• 1.1·10−15 97 CACNA1I Voltage-dependent T-type calcium channel subunit DA 22+ 40058440 40060743 2303 GGGGCGGGGCC GGCCTCGCCCC 11 29.3 • • • • • • • • • ◦ 1.1·10−27 98 CACNA2D2 Voltage-dependent calcium channel subunit AD exon 3− 50402615 50402505 110 GGGGGCGGGG CCCCGCCCTC 10 25.9 •••••◦•••• ◦ 5.2·10−23 99 CACNB1 Voltage-dependent L-type calcium channel subunit DA 17− 37342202 37341403 799 GGGAAGGGGG TCCCCTTCCC 10 23.4 • • ◦ • • • • • • • 1.4·10−13 100 CADPS Calcium-dependent secretion activator 1 isoform DD trans 3− 62467397 62423778 43619 CATATTTTG CAAAATGTG 9 10.4 • • • • • • • • • ◦ 5.4·10−6 101 CADPS Calcium-dependent secretion activator 1 isoform AD 3− 62498443 62479319 19124 CTCTCTTCT AGAAGAGAG 9 16.5 • • • • • • • • ◦ • 6.2·10−7 102 CADPS Calcium-dependent secretion activator 1 isoform AD 3− 62502318 62498425 3893 CAGATTAAC GTTAATTTG 9 10.4 ••◦••••••• ◦ 1.7·10−16 103 CADPS Calcium-dependent secretion activator 1 isoform DD cis 3− 62423778 62423778 0 CAAAATGTGAC GTCACATTTTG 11 16.9 • • • • • • • • • ◦ 2.4·10−6 104 CADPS Calcium-dependent secretion activator 1 isoform DA 3− 62522170 62502318 19852 TGATTCCTAT ATAGGAATCA 10 16.7 ••••••••◦• ◦ 8.0·10−15 −9 105 CADPS Calcium-dependent secretion activator 1 isoform DD cis X 3− 62498425 62498425 0 GCTCCTTAA TTAAGGAGT 9 15.5 ••◦••••••• • 2.2·10 106 CADPS Calcium-dependent secretion activator 1 isoform DA 3− 62479319 62467544 11775 GAAAGAAGA TTTTCTTTC 9 11.5 • • • • • • • • ◦ • 1.1·10−11 107 CADPS Calcium-dependent secretion activator 1 isoform AD 3− 62498443 62423778 74665 GCATTTTGG CCAAAATGT 9 13.8 • • • • • • • • • ◦ 5.9·10−6 108 CAMK2A Calcium/calmodulin-dependent protein kinase type AD 5− 149624764 149607754 17010 GCCCTGCCTG CGGGCAGGGC 10 24.4 • • ◦ • • • • • • • 7.8·10−14 109 CAMK2A Calcium/calmodulin-dependent protein kinase type DD trans 5− 149631544 149619266 12278 CCTCTCTCC GGGGAGAGG 9 19.2 ••◦••••••• ◦ 1.3·10−18 110 CAMK2A Calcium/calmodulin-dependent protein kinase type AD 5− 149630373 149607754 22619 CCCTGCCTG CGGGCAGGG 9 21 •••••••••• ◦ 9.7·10−17 111 CAMK2A Calcium/calmodulin-dependent protein kinase type AA trans 5− 149631628 149630373 1255 GGGCAGGGG CCCCTGCCT 9 22.9 • • ◦ • • • • • • • 2.8·10−17 112 CAMK2A Calcium/calmodulin-dependent protein kinase type AD 5− 149631628 149607754 23874 CTGCCTGTC GACGGGCAG 9 19 • • • • • • ◦ • • • 3.9·10−15 113 CAMK2D Calcium/calmodulin-dependent protein kinase type DA 4− 114530307 114424133 106174 GTAAGTATA TGTACTTAC 9 12.4 • • • • • • • ◦ • • 6.7·10−17 7 −14 114 CAMK2G Calcium/calmodulin-dependent protein kinase type AD exon X 10− 75599359 75599296 63 GGCATGCTC GGGCATGCC 9 19 •••••••◦••◦◦ 1.4·10 115 CAMK2G Calcium/calmodulin-dependent protein kinase type AD 10− 75583842 75579289 4553 TCTCTCACA TGTGAGGGA 9 16.9 • • • • • • • • • ◦ 2.3·10−19 116 CAMK2G Calcium/calmodulin-dependent protein kinase type DD trans 10− 75601926 75599296 2630 GGTGAGTGG CCACTCACC 9 19.7 •••••••◦••◦◦ 8.4·10−24 117 CAMK2G Calcium/calmodulin-dependent protein kinase type DD trans 10− 75599296 75576780 22516 GCCCACTCAC GTGAGTGGGT 10 22.2 ••••••••••◦◦ 5.7·10−17 118 CAMK2G Calcium/calmodulin-dependent protein kinase type DA 10− 75601926 75579403 22523 AGGTGAGTG CGCTCACCT 9 18.1 ••••• ••••◦◦ 1.9·10−24 119 CAMSAP1L1 Calmodulin-regulated -associated protein DA intron 1+ 200822623 200823944 1321 AAGAGTCTGTTCAT ATGAACAGACTCTT 14 25 ••••◦••◦••• 5.5·10−19 120 CAPRIN1 Caprin-1 isoform 2 AA cis 11+ 34120849 34120849 0 GAAGGCAAA TTTGTCTTC 9 13.3 ••••• ••••◦◦ 3.4·10−6 121 CASK Peripheral plasma CASK isoform DA X− 41481869 41394039 87830 TGTTTTCCT AGGAAAACA 9 14.8 •••••••••• ◦ 7.3·10−19 122 CASK Peripheral plasma membrane protein CASK isoform AA trans X− 41416353 41414888 1465 GTGTTCTGT ACAGAACAC 9 16.2 ••◦••••••• ◦ 5.8·10−11 −20 123 CBFA2T3 Protein CBFA2T3 isoform 1 AD exon X 16− 88964560 88964485 75 TTTGCTTAC GTAAGTAAA 9 11.8 ••••••••• 2.9·10 124 CCDC85A Coiled-coil domain-containing protein 85A AA cis 2+ 56602950 56602950 0 AACGACTTT AAAGTTGTT 9 11.9 •••••••◦•• ◦ 9.9·10−11 125 CCDC88A Girdin isoform 2 AD 2− 55529208 55518811 10397 CATTTGCAT ATGTAAATG 9 11.7 • • • • • • • ◦ • • 6.8·10−13 126 CCNG1 -G1 DD cis 5+ 162864665 162864665 0 CCCTCCCCGGGCCT AGGCCCGGGGAGGG 14 38.8 ••••••••• 4.4·10−7 127 CCNL1 Cyclin-L1 AA trans 3− 156870945 156870030 915 AAGGGAAAA TTTTCCCTT 9 14.7 •• ••••◦••◦• 4.8·10−15 128 CCNL1 Cyclin-L1 AD 3− 156870945 156869965 980 GAAGGGAAAA TTTTCCCTTT 10 16 ••••••••••◦◦ 1.0·10−10 129 CD19 B-lymphocyte antigen CD19 isoform 1 precursor AD 16+ 28944231 28950089 5858 TCTGCATTT AGATGCAGA 9 15.1 • • • • • • • • • ◦ 3.9·10−20 130 CD4 N/A AD 12+ 6925221 6928080 2859 TCCCTTCCC GGGGAGGGA 9 20.5 • • ◦ • • • • • • • 2.5·10−25 131 CD4 N/A AD exon 12+ 6928012 6928080 68 CCTCCCTTC GAAGGGAGG 9 19.8 ••••••••• 7.7·10−19 132 CDH12 Cadherin-12 preproprotein AA cis 5− 21783603 21783603 0 ATAAAGAAG CTTCTTTAT 9 11.7 •••••••••• ◦ 8.6·10−7 133 CDH23 Cadherin-23 isoform 3 DD trans 10+ 73553397 73555836 2439 CTTCTCTCC GGAGAGGAG 9 17.2 •••••••••• 1.1·10−19 134 CDH23 Cadherin-23 isoform 3 AD 10+ 73550044 73553397 3353 GGGGGCTGGG CCCAGCTCCC 10 24.4 ••••• •••••◦ 4.1·10−22 135 CDK13 Cell division protein kinase 13 isoform 2 AD 7+ 40038959 40102526 63567 ATTTGCTTG CAAGCAAAT 9 13.5 ••••••••• 1.1·10−13 136 CDK16 Cell division protein kinase 16 isoform 1 DD trans X+ 47084142 47085265 1123 CCCACAGTC GACTGTGGG 9 19.7 ••••◦•••••◦ 2.0·10−22 137 CDK16 Cell division protein kinase 16 isoform 1 DA X+ 47084289 47085363 1074 CAAAGGCAA TTGTCTTTG 9 13 •••••••••• ◦ 9.0·10−21 Supplementary Table 1: (continued)

138 CDK16 Cell division protein kinase 16 isoform 1 DD trans X+ 47085265 47086498 1233 AGGACAAGG CTTTGTCCT 9 15.7 ••◦•••◦•••• 4.9·10−21 139 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 AA trans 9− 123298804 123199805 98999 GAAAAATTG CAATTTTTC 9 10.1 • • • • ◦ • • • • • 4.8·10−10 140 CDK5RAP2 CDK5 regulatory subunit-associated protein 2 AD 9− 123298804 123220727 78077 TTCCTTTCA TGGAAGGAA 9 14.5 • • • • • ◦ • • • • 9.7·10−13 141 CDK8 Cell division protein kinase 8 AA trans 13+ 26956950 26975602 18652 TTTGTTTCC GGAGACAAA 9 13.7 ••••••••••◦◦ 7.8·10−19 142 CDKL5 Cyclin-dependent kinase-like 5 DD cis X+ 18646707 18646707 0 TCCTCTGTG CACAGAGGG 9 17.8 •••••••••◦ ◦ 9.4·10−5 −7 143 CELF2 CUGBP Elav-like family member 2 isoform 2 AA cis X 10+ 11372418 11372418 0 AATGCAAATT GATTTGCATT 10 13.8 •••••••••••• 3.0·10 144 CELF2 CUGBP Elav-like family member 2 isoform 2 AD 10+ 11291115 11371060 79945 TCTGCCTTT GAAGGCAGA 9 17.6 ••••◦••••• ◦ 3.1·10−20 145 CELF2 CUGBP Elav-like family member 2 isoform 2 DA 10+ 11259470 11372418 112948 GAATCACTTT AAAGTGATTT 10 13.9 •◦◦••••••••◦ 9.2·10−14 146 CELF4 CUGBP Elav-like family member 4 isoform 1 DA 18− 34846495 34825160 21335 GAGGGAGGG CCTTCCCTC 9 19.5 • ◦ • • • • • • • • 2.4·10−16 147 CELSR3 Cadherin EGF LAG seven-pass G-type receptor 3 DD trans 3− 48682875 48682467 408 AGGTTGGGG CCCCAACCT 9 20.5 •••••••••• 4.0·10−20 148 CELSR3 Cadherin EGF LAG seven-pass G-type receptor 3 DD trans 3− 48686151 48682875 3276 CCTTGGCCC GGGCCAGGG 9 21.4 ••••••••• 1.5·10−15 −2 149 CFL2 Cofilin-2 DD cis X 14− 35182713 35182713 0 TCTTCTACA TGTAGAGGA 9 15.2 •◦••••••••◦◦ 5.5·10 150 CGGBP1 CGG triplet repeat-binding protein 1 DD cis 3− 88190119 88190119 0 TTATCTTGA TCAAGGTAA 9 12.6 ••••••••• 3.7·10−1 151 CHD4 Chromodomain-helicase-DNA-binding protein 4 AD 12− 6692279 6687194 5085 GGCAAAGGA TCCTTTGCC 9 18.4 ••◦••••••• ◦ 1.1·10−12 152 CHD4 Chromodomain-helicase-DNA-binding protein 4 DD cis 12− 6692192 6692192 0 CCGTAGGCC GGCCTGCGG 9 21.3 ••••••••••◦ 1.0·10−14 153 CHD4 Chromodomain-helicase-DNA-binding protein 4 DD trans 12− 6709699 6692363 17336 GGGGGGTGGGG CCCCGCCCCCC 11 30.3 • • • • • • • ◦ • • 1.9·10−7 154 CHD9 Chromodomain-helicase-DNA-binding protein 9 DD cis 16+ 53341817 53341817 0 AGAAGCATG CATGCTTTT 9 13.6 •••••••••••◦ 2.6·10−5 155 CHIC2 Cysteine-rich hydrophobic domain 2 protein AD exon 4− 54880286 54880229 57 CATTTGTCT GGACAAATG 9 13.8 ••◦••••••◦ • 1.1·10−13 156 CHRND Acetylcholine receptor subunit delta precursor DD trans 2+ 233396173 233398845 2672 GTTCCTGCT AGCAGGAAC 9 18.5 ••◦•••••◦••◦ 8.6·10−29 157 CIT Citron Rho-interacting kinase DD cis 12− 120221711 120221711 0 TGTGTCTCAT ATGAGGCACA 10 18.1 •••••••••• ◦ 4.0·10−10 158 CLINT1 Clathrin interactor 1 isoform 1 DD trans 5− 157244450 157241192 3258 AATTTGCTT AAGCAAATT 9 12.3 •••••••◦•• ◦ 4.1·10−13 159 CLK4 Dual specificity protein kinase CLK4 AD exon 5− 178044435 178044344 91 CTCCCCGCTGA TCAGCGGGGGG 11 25.9 •••••••••••◦ 4.6·10−6 8 160 CLSTN3 Calsyntenin-3 precursor DD trans 12+ 7285742 7295622 9880 GAGGGAGGGA TCCCTTCCTC 10 21.7 ••••••••••• 4.5·10−22 161 CLSTN3 Calsyntenin-3 precursor DD trans 12+ 7283308 7295622 12314 GGGGGTGGGG CCCCACCCCC 10 27.4 • • • ◦ • • • • • • 5.7·10−20 162 CLSTN3 Calsyntenin-3 precursor DA 12+ 7285742 7290550 4808 AAGGAGGGG CCTCTCCTT 9 17.7 •••••••◦•• ◦ 2.3·10−24 163 CNOT2 CCR4-NOT transcription complex subunit 2 DD cis 12+ 70723350 70723350 0 TGGACCAGAA TTCTGGTTCA 10 17.9 ••••••◦••••◦ 3.3·10−12 164 COG3 Conserved oligomeric Golgi complex subunit 3 DD cis 13+ 46090398 46090398 0 GCTGGCACA TGTGTCAGC 9 18 ••••◦••••• ◦ 4.9·10−9 165 COL12A1 Collagen alpha-1(XII) chain short isoform AA trans 6− 75904663 75796273 108390 TTATGCAAA TTTGCATAG 9 12.4 ◦◦•••••••• • 2.9·10−14 166 COL16A1 Collagen alpha-1(XVI) chain precursor AD 1− 32145286 32122000 23286 GTCTCCTCT AGAGGAGAC 9 19 ••◦••••••• ◦ 2.4·10−25 167 COL17A1 Collagen alpha-1(XVII) chain AD 10− 105820038 105799202 20836 TCTTTCTCC GGAGAGAGA 9 16.6 ••••••••• 9.4·10−18 −9 168 COL6A3 Collagen alpha-3(VI) chain isoform 4 precursor AA cis X 2− 238296827 238296827 0 CGTGTTTCTT AAGAAACATG 10 14.3 •••••••••◦•• 9.9·10 169 COL7A1 Collagen alpha-1(VII) chain precursor AD 3− 48616948 48605142 11806 CTCCCTGGAG CTCCAGGGGG 10 22.2 •••••••••• 1.1·10−18 170 COL7A1 Collagen alpha-1(VII) chain precursor DD trans 3− 48621917 48605142 16775 CCCCCTGGA TCCAGGGGG 9 23.1 • • • • • • ◦ • • • 1.6·10−20 171 COL7A1 Collagen alpha-1(VII) chain precursor DD trans 3− 48619138 48605142 13996 CCCTGGAGA TCTCCAGGG 9 21 • • ◦ • • • • • • • 2.4·10−19 172 CPEB2 Cytoplasmic element-binding DA 4+ 15009210 15042087 32877 GTATGTAAA TTTACATGC 9 12 ••••◦••◦••• 9.4·10−20 173 CPEB3 Cytoplasmic polyadenylation element-binding DA 10− 93952302 93851701 100601 TTGCTTGGT ACCAAGTAA 9 15 • • • • • • • • • ◦ 1.4·10−9 174 CPEB3 Cytoplasmic polyadenylation element-binding AD 10− 94000118 93952302 47816 TGAAACACC GGTGTTTTA 9 13.9 •••••••◦•• ◦ 5.2·10−11 175 CPNE1 RNA-binding protein 12 AD 20− 34246936 34243123 3813 GCCTGTGCGT GCGCACAGGT 10 22.6 •••••••••• ◦ 2.3·10−9 176 CREBBP CREB-binding protein isoform a AA cis 16− 3801807 3801807 0 TGCTTGGGTGG TCACCCAAGTA 11 21 ••••••••••◦◦ 1.9·10−2 177 CRTAC1 Cartilage acidic protein 1 precursor DA 10− 99661259 99655170 6089 GGGAGAAGG TCTTCTCCC 9 18 • • • • • • • • • ◦ 2.0·10−22 178 CSNK1A1 Casein kinase I isoform alpha isoform 1 AD 5− 148897440 148885009 12431 AATACTGTT AACAGTGTT 9 12.8 ••••••••••• 9.0·10−6 179 CSNK1A1 Casein kinase I isoform alpha isoform 1 AA trans 5− 148929744 148897440 32304 GATGCCATC GATGGCATT 9 16.8 ••◦••••••• ◦ 1.0·10−11 180 CSNK1G1 Casein kinase I isoform gamma-1 DD trans 15− 64499707 64472546 27161 CCTTGAAAG CTTTCAAGG 9 14.7 ••◦•••••••◦◦ 1.0·10−26 181 CSTF3 Cleavage stimulation factor subunit 3 isoform 2 DD cis 11− 33163430 33163430 0 TCTATGGGT ACCTATAGA 9 15.5 ••••• •••••◦ 1.3·10−1 182 CTNNB1 beta-1 DA intron 3+ 41280845 41281309 464 CTTGGTTGG CTAACCAAG 9 14.6 ••◦••••◦•••◦ 4.9·10−10 183 CTNNB1 Catenin beta-1 DA 3+ 41265572 41281309 15737 CATTTTCTG CAGAAAGTG 9 12.5 ••◦•••••••◦ 6.8·10−9 Supplementary Table 1: (continued)

184 CUL4B Cullin-4B isoform 2 AA trans X− 119694480 119677664 16816 TTTCTTCCC GGGAGGAAA 9 15.9 • • • • ◦ • • • • • 1.0·10−6 185 CUL7 Cullin-7 isoform 1 DD trans 6− 43007893 43006579 1314 GGGGTTGGG CCCAGCCCC 9 21.7 • ◦ • • • • • • • • 4.5·10−22 186 CUL9 Cullin-9 DD trans 6+ 43174248 43181032 6784 AGGAAGAGG CCTCTTCCT 9 18.6 • • • • • • ◦ • • • 3.2·10−23 −10 187 CUX1 Protein CASP isoform a AD exon X 7+ 101842081 101842147 66 TTGTTTTTC GAAAAACAG 9 10.9 • • • • • • • • • ◦ 1.0·10 188 CYP7B1 25-hydroxycholesterol 7-alpha-hydroxylase AD exon 8− 65527789 65527582 207 CTGTGTCCT AGGACACAG 9 18.5 ••◦•••••◦••◦ 2.6·10−7 189 CYP7B1 25-hydroxycholesterol 7-alpha-hydroxylase AA cis 8− 65527789 65527789 0 TGCACTGAT ATCAGTGTA 9 15.5 ••••••••••◦◦ 7.7·10−1 190 DACH1 Dachshund homolog 1 isoform c AA trans 13− 72256042 72063280 192762 TTGTTTGTTT AAACAGACAA 10 13.2 ••••••••••• 1.0·10−1 191 DACH1 Dachshund homolog 1 isoform c AA cis 13− 72256042 72256042 0 TTGAAACAAAT GTTTGTTTCAG 11 14.4 •••••••••••◦ 9.7·10−1 −11 192 DCTN1 subunit 1 isoform 5 DA intron X 2− 74601449 74600075 1374 GGCAGCAGG CCTGTTGCC 9 19.4 • • • • • • • ◦ • • 4.0·10 193 DCTN1 Dynactin subunit 1 isoform 5 DA 2− 74601449 74593502 7947 TTGCTTGCT AGCAAGCGA 9 16.7 • • • • • • • • ◦ • 2.0·10−13 194 DCTN1 Dynactin subunit 1 isoform 5 DA 2− 74603868 74600075 3793 GCCAGAGGA TCTTCTGGC 9 18.4 •••••••••◦ ◦ 3.0·10−15 −14 195 DCTN1 Dynactin subunit 1 isoform 5 DA intron X 2− 74604558 74601467 3091 AGGAGGGATA TGTCCCTCCT 10 21.3 •••••••••• 1.4·10 196 DCTN1 Dynactin subunit 1 isoform 5 AD 2− 74601467 74590420 11047 CTTCGTCTG CAGATGAAG 9 14.8 • • • • • • ◦ • • • 3.5·10−15 197 DCTN1 Dynactin subunit 1 isoform 5 DA 2− 74601449 74593145 8304 GGGGGTGGG CTCACCCCC 9 21.1 • • ◦ • • • • • • • 5.4·10−18 198 DDX42 ATP-dependent RNA helicase DDX42 AA trans 17+ 61876948 61877827 879 TGCAGGGAAG CTTTCCTGCA 10 18.8 ••••• •••••◦ 1.9·10−19 199 DDX42 ATP-dependent RNA helicase DDX42 AA cis 17+ 61876948 61876948 0 TTAGTGTTGA TCAACACTAA 10 16.2 ••••• ••••◦◦ 4.7·10−8 200 DDX5 Probable ATP-dependent RNA helicase DDX5 DA intron 17− 62498127 62496891 1236 TGTGGCAAG TTTGCCACA 9 16.7 •••••◦•••• ◦ 1.7·10−5 201 DENND1A DENN domain-containing protein 1A isoform 2 AA trans 9− 126371760 126213028 158732 TCTGTTTCT GGAAACAGA 9 15.1 •••••••••• 6.7·10−4 202 DENND1A DENN domain-containing protein 1A isoform 2 AD exon 9− 126213028 126212971 57 TTTCATGCA TGTATGAAA 9 13 ••••••◦•◦• • 1.3·10−10 203 DENND1A DENN domain-containing protein 1A isoform 2 AA trans 9− 126433650 126371760 61890 TTTCTTTCA TGAAAGGAA 9 12.1 •••••••••• 3.9·10−11 204 DENND1A DENN domain-containing protein 1A isoform 2 AA trans 9− 126554909 126213028 341881 ATCATCTTCT AGAAGGTGAT 10 16 •••••••••• 6.5·10−3 205 DENND1A DENN domain-containing protein 1A isoform 2 DA 9− 126554865 126433650 121215 CTGAAAGAGA TTTCTTTCAG 10 14.8 •••••••••• 1.0·10−11 9 206 DENND1A DENN domain-containing protein 1A isoform 2 AA trans 9− 126414402 126213028 201374 TTCTGATTAT GTAATCAGAG 10 14.3 • • • • • ◦ • • • • 6.1·10−14 207 DENND1A DENN domain-containing protein 1A isoform 2 AA cis 9− 126554909 126554909 0 ATAGCAGCCT GGGCTGCTAT 10 20.9 ••••••••••◦ 9.9·10−1 208 DENND1A DENN domain-containing protein 1A isoform 2 AA trans 9− 126531842 126520101 11741 TTGATAAAG CTTTATCAA 9 11.7 • • ◦ • • • • • • • 4.6·10−8 209 DGKZ Diacylglycerol kinase zeta isoform 4 AD 11+ 46393253 46396389 3136 GGCCCCAGG CCTGGGGCC 9 24.1 •••••••••• 2.1·10−17 210 DHX15 Putative pre-mRNA-splicing factor ATP-dependent DA intron 4− 24541730 24538796 2934 ATAGAGGGA TTCCTCTAT 9 15.1 ••••◦••◦•••◦ 1.9·10−12 −5 211 DLG2 Disks large homolog 2 isoform 2 AA cis X 11− 83195271 83195271 0 CTAGTTGTT AACAATTAG 9 11.5 ••••••••••• 3.6·10 212 DLG4 Disks large homolog 4 isoform 1 DD trans 17− 7120436 7096263 24173 TGGGGAGGGG CCTCTCCCCA 10 23.4 ••••••••• 2.3·10−10 213 DLG4 Disks large homolog 4 isoform 1 DD trans 17− 7096801 7096263 538 GAGAAGGGG CTCCTTCTC 9 16.8 ••••◦•◦••• • 3.7·10−20 214 DLGAP4 Disks large-associated protein 4 isoform c DD trans 20+ 35128079 35154409 26330 CTGGATTTC GAAGTCCAG 9 15.2 •••••••••• 2.0·10−6 215 DNAH11 heavy chain 11, axonemal AA trans 7+ 21730382 21827018 96636 GCATTTGTC GATAAATGC 9 13.2 • • • • • • • • • ◦ 1.1·10−9 216 DOCK9 Dedicator of cytokinesis protein 9 isoform b AA trans 13− 99519790 99498245 21545 TTCCTGCAG TTGCAGGAA 9 16.9 ••◦•••••••◦◦ 3.9·10−23 217 DPP10 Inactive dipeptidyl peptidase 10 isoform short DD trans 2+ 116447315 116548755 101440 AAGGGAAGT ACTTCCTTT 9 14.5 ••••••••• 1.9·10−11 218 DRP2 -related protein 2 isoform 1 DA X+ 100475135 100496656 21521 TGTGTGTGT GCACACACA 9 17.5 • • ◦ • • • • • • • 4.4·10−21 219 DVL1 Segment polarity protein dishevelled homolog DD trans 1− 1277742 1274741 3001 TGCTGGGGC GCCCCAGCA 9 23 • ◦ • • • • • • • • 2.4·10−24 220 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 AA trans 2+ 172563056 172582703 19647 TCTTTGTCT AGACAAAGA 9 15.1 ••••••••• 2.7·10−10 221 DYNC1I2 Cytoplasmic dynein 1 intermediate chain 2 DD trans 2+ 172563074 172583426 20352 CTGTTTGCA TGCAAACAG 9 15.8 ••••••••• 5.7·10−8 222 EBF1 Transcription factor COE1 DA 5− 158511673 158223483 288190 AAAGAGAAG CTTCTCTTT 9 13.8 ••◦••••••• ◦ 2.0·10−18 223 EBF1 Transcription factor COE1 DD trans 5− 158500403 158223352 277051 AACACCTGC GTAGGTGTT 9 16.3 ••••••••••• 1.4·10−16 224 EBF3 Transcription factor COE3 DA intron 10− 131639107 131638598 509 GGCTGGGCG CGTCCAGCC 9 20.6 •◦•••••••• ◦ 1.2·10−11 225 EBF3 Transcription factor COE3 DA 10− 131760434 131638598 121836 TGAGAAAGT ATTTTCTCA 9 12.8 •••••••••• 7.3·10−12 226 EDC4 Enhancer of mRNA-decapping protein 4 AD 16+ 67912262 67916230 3968 GTCAAGTTCTG CAGAACTTGAC 11 19.4 • • ◦ • • • • • • • 3.2·10−18 227 EFNB3 Ephrin-B3 precursor DA intron 17+ 7612057 7612484 427 AGGAAAGAG CTCTTTCCT 9 16.2 •••••◦•◦•••◦ 4.8·10−23 228 EGFL8 Epidermal growth factor-like protein 8 DD trans 6+ 3395063 3395802 739 GGGGGTGGGG CCCCGCCCCC 10 27 •••••◦••••◦ 4.1·10−28 229 EHBP1 EH domain-binding protein 1 isoform 2 AD 2+ 63085540 63223901 138361 CTGTTTACAG CTGTAAACAG 10 15.9 ••••••••• 4.6·10−6 Supplementary Table 1: (continued)

−11 230 EIF4G1 Eukaryotic translation initiation factor 4 gamma DA intron X 3+ 184032462 184033276 814 CCCCACCCCC GGGGGTGGGG 10 27.4 • • • • • • • • ◦ • 4.5·10 −3 231 EIF4G1 Eukaryotic translation initiation factor 4 gamma AA cis X 3+ 184033276 184033276 0 TGGGGGGTG CACCTCCCA 9 19.9 •••••••••• 1.2·10 232 EIF4G1 Eukaryotic translation initiation factor 4 gamma AD 3+ 184033276 184033644 368 GGGGGTGGG CCTACCCCC 9 21.8 •••••••••• 2.1·10−10 233 EIF4G2 Eukaryotic translation initiation factor 4 gamma DD trans 11− 10825833 10820759 5074 TAATTTCCA TGGAAATTA 9 12.9 ••••••••◦• ◦ 1.8·10−23 234 EIF4G3 Eukaryotic translation initiation factor 4 gamma DD cis 1− 21205815 21205815 0 TATTCTCCCCT AGGGGAGAATA 11 22.2 • • • • • • • • • ◦ 4.7·10−10 −9 235 ELAVL4 ELAV-like protein 4 isoform 5 DA intron X 1+ 50663139 50666480 3341 GGCACAGAC GTCTGTGTC 9 17.1 • • • • • • • • • ◦ 1.6·10 236 ELAVL4 ELAV-like protein 4 isoform 5 DA 1+ 50569672 50663100 93428 CAGATGGTA TGCCATCTG 9 16.6 • • • • • • ◦ • • • 4.2·10−5 237 EMID1 EMI domain-containing protein 1 AD exon 22+ 29650191 29650276 85 TCTGTCTCT AGAGACAGA 9 17.8 •••••••••• 1.1·10−11 238 ENOX1 Ecto-NOX disulfide-thiol exchanger 1 AA cis 13− 43900661 43900661 0 GATGATGTT GACATCATC 9 14.7 ••••••••••◦• 9.7·10−4 239 EPHA4 Ephrin type-A receptor 4 precursor AD 2− 222433505 222428450 5055 TATTGGCTT AAGCCAGTA 9 15.1 ••••• ••••◦◦ 3.5·10−17 240 EPHA4 Ephrin type-A receptor 4 precursor DD trans 2− 222433437 222307548 125889 TAATGGCTTG CAAGTCATTA 10 14.5 ••••• ••••◦◦ 6.1·10−15 241 EPHA7 Ephrin type-A receptor 7 precursor AA trans 6− 94066770 93969197 97573 AAGAAAGCAT ATGCTTTCTT 10 15.9 • • ◦ • • • • • • • 4.7·10−8 242 EPHA7 Ephrin type-A receptor 7 precursor AA trans 6− 94066770 93982140 84630 GAAAGAAAGCA TGCTTTCTTTT 11 17 •••••••••• 1.9·10−8 243 ERBB4 Receptor tyrosine-protein kinase erbB-4 isoform AD 2− 212537982 212522478 15504 AGATGTTAC GTAACATCT 9 14.3 ••••• ••••◦◦ 1.2·10−21 −20 244 ERBB4 Receptor tyrosine-protein kinase erbB-4 isoform AD exon X 2− 212252717 212252669 48 TCACTGTTG CAACAGTGA 9 16.1 •••••◦◦••••◦ 2.4·10 245 ERBB4 Receptor tyrosine-protein kinase erbB-4 isoform AA trans 2− 212522553 212252717 269836 TGATGGATA TATCCATCA 9 15.8 ••••• •••◦•◦ 1.8·10−14 246 ERCC2 TFIIH basal transcription factor complex DD trans 19− 45873793 45867243 6550 GGGGCTGGG CCCAGTCCC 9 21.4 • ◦ • • • • • • • • 2.7·10−22 247 ERI3 ERI1 exoribonuclease 3 AD 1− 44804994 44778840 26154 GGGAGGGAG CTCCCTCCC 9 22.2 •••••••••• ◦ 4.8·10−12 248 ERI3 ERI1 exoribonuclease 3 DD trans 1− 44804716 44778840 25876 GGGAGGGAG CTCCCTCCC 9 22.2 •••••••◦•• ◦ 1.7·10−14 249 ESRP1 Epithelial splicing regulatory protein 1 isoform DA 8+ 95686722 95709079 22357 ATGTAAGTT AACTTGCAT 9 12.8 • • • • • • • • • ◦ 1.0·10−14 250 EWSR1 RNA-binding protein EWS isoform 1 DD cis 22+ 29684775 29684775 0 CATTTCCATG CATGGAAATG 10 16 ••••••••••◦◦ 3.7·10−7 −1 10 251 EWSR1 RNA-binding protein EWS isoform 1 AA cis X 22+ 29687550 29687550 0 AGCCAGTGCC GGTACTGGCT 10 22 ••••••••••◦◦ 9.0·10 252 EWSR1 RNA-binding protein EWS isoform 1 AD 22+ 29686401 29687588 1187 ATGGTTTTC GAAAACTAT 9 11.5 ••••••••◦•◦ 2.1·10−4 253 EWSR1 RNA-binding protein EWS isoform 1 DA 22+ 29670271 29687550 17279 CATCTTGTC GACAAGATG 9 15.3 •••••••••• ◦ 4.6·10−7 254 EWSR1 RNA-binding protein EWS isoform 1 DA 22+ 29684775 29688125 3350 GCAAACCTT AAGGTTTGT 9 14.9 ••◦••••••••◦ 1.6·10−12 255 EXOC6 Exocyst complex component 6 isoform a AA cis 10+ 94654550 94654550 0 CAAGTTCAA TTGAATTTG 9 11.3 •••••••••••◦ 1.7·10−1 −12 256 EYA4 Eyes absent homolog 4 isoform d AD exon X 6+ 133846152 133846253 101 TGCATTGTT AATAATGCA 9 12.9 ••••••◦◦•• • 5.0·10 257 EYA4 Eyes absent homolog 4 isoform d AD 6+ 133783472 133846253 62781 ATTTTTCTG CAGAAAAGT 9 11.3 •••••••••• ◦ 2.3·10−10 −9 258 EYA4 Eyes absent homolog 4 isoform d AD exon X 6+ 133846291 133846392 101 CACTAACAT ATGTTGGTG 9 13.7 ◦•••••◦••• • 1.1·10 259 FAF1 FAS-associated factor 1 AD exon 1− 51171563 51171457 106 TAGCTGTAA TTATAGCTA 9 13.5 • • • • ◦ • • • • • 2.6·10−6 260 FAF1 FAS-associated factor 1 AD 1− 51253877 51171457 82420 GTCAACATT AATGTTGAC 9 13.9 • • • • • • • • • ◦ 5.2·10−14 261 FAM108B1 Abhydrolase domain-containing protein FAM108B1 DD cis 9− 74481714 74481714 0 GCAAATCAT ATGATTTGT 9 13.1 •••••••••• ◦ 3.0·10−2 262 FAM171A2 Hypothetical protein LOC284069 precursor AD exon 17− 42437500 42437272 228 CCCCTCCCTC GAGGGGGGGG 10 24.6 • • • • • • • • • ◦ 1.6·10−18 263 FAM98A Hypothetical protein LOC25940 DD cis 2− 33813401 33813401 0 CCTTTAGTAC GTATTAAAGG 10 14 ••••••••••◦◦ 2.0·10−9 264 FAM98A Hypothetical protein LOC25940 AA trans 2− 33812387 33810511 1876 TTGATGGCA TGCCATCAA 9 17.4 •••••••◦••◦◦ 7.3·10−18 265 FAP Seprase AD 2− 163039978 163029658 10320 TAAACAAAG CTTTGTTTA 9 11.3 • • • • • • • • • ◦ 1.3·10−9 266 FAP Seprase AD exon 2− 163029731 163029658 73 CTCTGACTCTTA TAAGAGTCAGGG 12 21.2 •••••••••◦ ◦ 5.8·10−7 267 FAP Seprase AA cis 2− 163029731 163029731 0 ATGTGTTGCT AGCAATACAT 10 16.3 •••••••••• ◦ 4.6·10−3 268 FBN1 -1 precursor DD trans 15− 48902924 48704765 198159 TTTTTTCAC GTGAAAAAG 9 10.9 • • ◦ • • • • • • • 5.3·10−15 269 FHOD1 FH1/FH2 domain-containing protein 1 DD trans 16− 67265539 67264503 1036 GTATGGAAC GTTCCATGC 9 15.5 • • • • • • ◦ • • • 1.1·10−18 270 FIGN Fidgetin AD exon 2− 164591582 164591412 170 AAATTGACAT ATGTCAGTTT 10 13.7 •••••◦•••• ◦ 6.8·10−10 271 FIP1L1 Pre-mRNA 3’-end-processing factor FIP1 isoform DD trans 4+ 54245284 54257665 12381 GAAGTTGAA TTCAGCTTC 9 13.9 • • • • • ◦ • • • • 4.6·10−9 −4 272 FIP1L1 Pre-mRNA 3’-end-processing factor FIP1 isoform DD cis X 4+ 54306775 54306775 0 TTTCATGTTT AAACATGAAA 10 13.5 • • ◦ • • • • • • • 1.2·10 273 FN1 Fibronectin isoform 1 preproprotein AA trans 2− 216295575 216251681 43894 CTGTTTTTC GAAAAACAG 9 12.4 ••••••••◦• ◦ 2.1·10−21 274 FN1 Fibronectin isoform 1 preproprotein DD cis 2− 216232585 216232585 0 CATGTTTGG CCAAACATG 9 14.7 •••••••••• ◦ 1.1·10−15 275 FNIP1 Folliculin-interacting protein 1 isoform 2 AD 5− 131046354 131039757 6597 TTTTTGCCA TGGCAGAAA 9 14.6 • • • • • • • • • ◦ 3.2·10−17 Supplementary Table 1: (continued)

276 FOSB Protein fosB isoform 1 AA cis 19+ 45973886 45973886 0 ACACACACATCCA TGGGTGTGTGTGT 13 25.5 ••••••••• 9.9·10−1 277 FOXP1 Forkhead box protein P1 isoform 2 DA 3− 71026793 71021827 4966 TTCTATAAG CTTATAGAA 9 12.1 •••••••◦•• ◦ 1.8·10−13 278 FOXP1 Forkhead box protein P1 isoform 2 AA trans 3− 71090683 71026873 63810 ATTTGTTTG CAGACAAAT 9 11.2 •••••••••• ◦ 3.0·10−15 279 FOXP1 Forkhead box protein P1 isoform 2 AD 3− 71090683 71019886 70797 GACGGAATTAG TTAATTCCGTT 11 16.4 •••••••••• ◦ 2.6·10−12 280 FOXP2 N/A AD 7+ 114269859 114299487 29628 AATGGTTTA TAAACCATT 9 12.7 • • • • • • • • • ◦ 1.7·10−10 281 FOXP2 N/A DD trans 7+ 114299487 114299728 241 TTTATGTCA TGACATAAG 9 12.7 • • ◦ • • • • • • • 8.0·10−8 282 FOXP2 N/A AA trans 7+ 114293980 114298120 4140 TCATTTCTA TAGAAGTGA 9 13.2 •••••••••• ◦ 4.4·10−7 283 FOXP2 N/A AD 7+ 114284739 114294064 9325 TTTTCTGACTG CAGTTAGAAAA 11 15.9 ••◦••••••• ◦ 1.6·10−7 284 FRYL Protein furry homolog-like AD 4− 48598017 48530191 67826 TCTTTTGTT AACAGAAGA 9 12.5 • • • • • • • • • ◦ 1.9·10−18 285 FST Follistatin isoform FST317 precursor AA cis 5+ 52781780 52781780 0 GCTGTTGTT AACAACAGC 9 15.9 ••◦•••◦••••• 5.2·10−6 286 FTO Alpha-ketoglutarate-dependent dioxygenase FTO AA cis 16+ 53967896 53967896 0 AAAAAAGCC GGCTTTTTT 9 13.3 •••••••••• 5.9·10−5 287 FTSJ3 Putative rRNA methyltransferase 3 AD 17− 61902097 61901690 407 CTTCCTCTCC GGAGAGGAAG 10 21 ••◦••••••• ◦ 3.4·10−23 −10 288 FUS RNA-binding protein FUS isoform 2 AD exon X 16+ 31198122 31198157 35 TTGGAAGCT AGTTTCCAA 9 14.8 •••••••◦••◦ 5.4·10 −8 289 FUS RNA-binding protein FUS isoform 2 DD cis X 16+ 31198157 31198157 0 AAGTGAACA TGTTCATTT 9 12.6 •••••••••••◦ 1.1·10 290 GAPVD1 GTPase-activating protein and VPS9 DA intron 9+ 128104578 128109097 4519 AGAGCACATATTTCA TGAGATATGTGCTCT 15 26.3 •••••••••• ◦ 3.9·10−10 291 GIGYF2 PERQ amino acid-rich with GYF domain-containing AA trans 2+ 233620932 233655967 35035 TTTTTTGGC GCCAAAGAA 9 13.4 •••••••••• ◦ 1.7·10−26 292 GIPR Gastric inhibitory polypeptide receptor DA intron 19+ 46180366 46180580 214 TCCCCACCCC GGGGTGGGGG 10 25.6 •••••••••• ◦ 1.0·10−9 293 GLCCI1 Glucocorticoid-induced transcript 1 protein DD cis 7+ 8124647 8124647 0 TGTCAGCTGGG TCCAGCTGATA 11 21.4 •••••••••◦ • 8.8·10−10 294 GLRA2 Glycine receptor subunit alpha-2 isoform B AD X+ 14592454 14592681 227 GCTTCAATG CATTGAAGC 9 15 • • • ◦ • • • • • • 4.6·10−15 295 GPAA1 Glycosylphosphatidylinositol anchor attachment 1 DA 8+ 145138206 145138841 635 GGCCTGGCT AGCCAGGCT 9 21.8 • • • • • • • • • ◦ 5.0·10−19 −24 296 GPM6A Neuronal membrane glycoprotein M6-a isoform 2 AD exon X 4− 176733400 176733341 59 AAGCAAACA TGTTTGCTT 9 14.6 ◦•••••••••◦◦ 9.7·10 −9 11 297 GPR162 Probable G-protein coupled receptor 162 isoform DD cis X 12+ 6932929 6932929 0 CCCCCACCCCC GGGGGTGGGGG 11 30.7 •••••••••• 1.7·10 298 GRIA2 Glutamate receptor 2 isoform 2 precursor AA trans 4+ 158262415 158282161 19746 CATACTTGT ACAAGTATG 9 14 ••••◦••••••• 2.6·10−18 −9 299 GRIA2 Glutamate receptor 2 isoform 2 precursor DA intron X 4+ 158281295 158282161 866 TCACAAAAA TTTTTGTGA 9 12.4 •••••••◦••◦◦ 1.0·10 300 GRIA2 Glutamate receptor 2 isoform 2 precursor DD trans 4+ 158281295 158284199 2904 GGTTTGTAT ATACAAACT 9 12.8 ••••◦•••••◦◦ 2.9·10−13 301 GRIA2 Glutamate receptor 2 isoform 2 precursor DD trans 4+ 158282276 158282804 528 GCAGCAGCT AGTTGCTGC 9 18.3 ••◦••◦•••••◦ 6.5·10−13 302 GRIA3 Glutamate receptor 3 isoform 2 precursor DD cis X+ 122598963 122598963 0 GTGGGTGGAATA TATTCCACCTAC 12 21.9 •••••••••• 9.3·10−1 −4 303 GRIA3 Glutamate receptor 3 isoform 2 precursor AD exon X X+ 122599524 122599639 115 TCTTGTGCTC GAGCACAAGA 10 19.7 ••••••••◦• ◦ 6.4·10 304 GRIA4 Glutamate receptor 4 isoform 1 precursor AA trans 11+ 105789437 105836673 47236 TCTCTCATT AATGAGAGG 9 14.6 •••••••◦•• ◦ 2.6·10−15 305 GRIA4 Glutamate receptor 4 isoform 1 precursor DD cis 11+ 105804695 105804695 0 GGTGGAATA TATTCCACC 9 16.6 •••••••••• 1.5·10−5 306 GRIA4 Glutamate receptor 4 isoform 1 precursor AD 11+ 105842640 105845171 2531 CTTTGCCAT GTGGCAAAG 9 16.2 •••••◦•••• ◦ 2.6·10−4 307 GRIK2 Glutamate receptor, ionotropic kainate 2 isoform DD cis 6+ 102337738 102337738 0 TTTTGGCAATT AATTGTCAAAA 11 13.8 •••••••••• 1.4·10−5 308 GRIK2 Glutamate receptor, ionotropic kainate 2 isoform DA 6+ 102511923 102513671 1748 GAAACATTT AAATGTTTC 9 11.4 ••••••••• 1.9·10−13 309 GRIK5 Glutamate receptor, ionotropic kainate 5 AA trans 19− 42566805 42525626 41179 CTGTGGAGA TCTCCACAG 9 18.7 •••••••••◦◦ 8.6·10−24 310 GRM4 Metabotropic glutamate receptor 4 precursor DD trans 6− 34024320 33995896 28424 GGGCCGGGCA TGCCTGGCCC 10 25.6 ••• •••••••◦ 1.2·10−29 311 GTDC1 Glycosyltransferase-like domain-containing DD trans 2− 144710339 144709548 791 TGTTAGTGT ACACTAACA 9 15.1 •••••••••••◦ 2.3·10−12 312 GTDC1 Glycosyltransferase-like domain-containing AD 2− 144969164 144728219 240945 CTTTAATGT GCATTAAAG 9 11.8 • • ◦ • • • • • • • 4.7·10−14 313 GTDC1 Glycosyltransferase-like domain-containing AD exon 2− 144709640 144709548 92 ACTAATATC GATATTAGT 9 12.4 ••◦••••••••◦ 4.7·10−6 314 GTDC1 Glycosyltransferase-like domain-containing AA trans 2− 144714906 144709640 5266 TCATTTTAC GTAAAGTGA 9 11.8 •◦••••••• •◦ 7.8·10−4 −14 315 H2AFY Core histone macro-H2A.1 isoform 2 AD exon X 5− 134686603 134686512 91 TGCGCACAC GTGTGTGCA 9 18 ••••••◦•••◦◦ 2.6·10 316 H2AFY Core histone macro-H2A.1 isoform 2 DD trans 5− 134688635 134686512 2123 AGCTGTCAG TTGACAGCT 9 17 ••••••••••◦◦ 5.4·10−21 317 HAT1 Histone acetyltransferase type B catalytic DA intron 2+ 172822429 172822929 500 TGAGTTTTC GAAAATTCA 9 11.6 ••◦••••••• ◦ 9.9·10−1 318 HAT1 Histone acetyltransferase type B catalytic DD trans 2+ 172779017 172822429 43412 GGGAAAAGT ATTTTTCCC 9 13.7 •••••••••• 1.7·10−8 319 HDAC1 Histone deacetylase 1 DD cis 1+ 32792678 32792678 0 GCCTGGCCT AGGCCAGGT 9 22.1 •••••••••• ◦ 1.5·10−7 320 HDAC1 Histone deacetylase 1 DA intron 1+ 32792678 32793136 458 TGCCTCCCT AGGGAGGCA 9 22 •••••••••• ◦ 1.0·10−11 −13 321 HDAC8 Histone deacetylase 8 isoform 1 DA intron X X− 71787738 71715118 72620 GTAAGAAAA TTTTCTTAC 9 11.6 ••••••••• 1.2·10 Supplementary Table 1: (continued)

322 HDAC9 Histone deacetylase 9 isoform 4 AA trans 7+ 18629958 18875089 245131 TCTTTCTCT GGAGAAAGA 9 15.3 ••••••••• 1.0·10−13 323 HDAC9 Histone deacetylase 9 isoform 4 DA 7+ 18706099 19035645 329546 AATAGGCAA TTGCCTGTT 9 15.1 •••••••••• 5.9·10−9 324 HDAC9 Histone deacetylase 9 isoform 4 AA trans 7+ 18535884 18832967 297083 GGGAGGAGGGA TCCCTCTTCCC 11 25.2 ••••••••••• 1.6·10−14 325 HDAC9 Histone deacetylase 9 isoform 4 AA trans 7+ 18832967 18875089 42122 CTTTCTCTC GGGAGAAAG 9 14.4 •••••••••• 1.0·10−16 326 HDAC9 Histone deacetylase 9 isoform 4 AD exon 7+ 18832967 18833075 108 CTTTCTTCT AGAAGGAAG 9 13.3 ••••◦••••• • 1.6·10−18 327 HDAC9 Histone deacetylase 9 isoform 4 DA 7+ 18535477 18875089 339612 TTCTTTTTC GAGAAAGAA 9 11.5 • • ◦ • • • • • • • 4.5·10−16 328 HDAC9 Histone deacetylase 9 isoform 4 AA trans 7+ 18767202 18875089 107887 CTCTTTTCTT AAGAAAAGAG 10 14.7 ••••••••• 9.2·10−14 329 HECTD1 E3 ubiquitin-protein ligase HECTD1 DD trans 14− 31602714 31597817 4897 AGGGAAAGC GCTTTTCCT 9 15.5 • • • • • • • • • ◦ 1.2·10−18 330 HECTD1 E3 ubiquitin-protein ligase HECTD1 DA 14− 31602714 31598654 4060 GGAAAGCAG CTGCTTTCT 9 16 • • • • • • • • • ◦ 2.7·10−15 331 HECW1 E3 ubiquitin-protein ligase HECW1 DD cis 7+ 43283531 43283531 0 CATTCCATTA TAATGGAATG 10 15.2 ••••••••• 5.3·10−5 332 HES7 Transcription factor HES-7 isoform 1 DA intron 17− 8025660 8025340 320 GGGGTGGGGC GCCCCGCCCC 10 27.1 ••••••••• 1.0·10−10 333 HES7 Transcription factor HES-7 isoform 1 AD exon 17− 8025748 8025660 88 TCCCTCCCTTC GGAGGGAGGGA 11 25 •••••••••••• 7.3·10−22 334 HES7 Transcription factor HES-7 isoform 1 DA 17− 8027360 8025748 1612 GGGAGGGGAGGG CCCTCCCCTCCC 12 32.1 ••••••••• 2.2·10−15 335 HIPK1 Homeodomain-interacting protein kinase 1 isoform DA intron 1+ 114506143 114508751 2608 TTTGCAGAGG TCTCTGCAAG 10 17.2 •••••◦•••••• 4.4·10−15 336 HIVEP1 protein 40 DD cis 6+ 12130125 12130125 0 AAATGTACATTTA TAAATGTACATTT 13 17 ••◦••••••• ◦ 3.9·10−11 337 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 AD 4− 83292737 83277948 14789 TTTTGATTGG CCAGTCAAAA 10 14.6 ••••••••• 2.1·10−5 338 HNRNPH1 Heterogeneous nuclear ribonucleoprotein H DD trans 5− 179046269 179045145 1124 AAATCCATA TATGGATTT 9 13.1 ••••• ••••◦◦ 3.8·10−21 339 HNRNPH1 Heterogeneous nuclear ribonucleoprotein H AD exon 5− 179046408 179046269 139 CTATAAGAA TTCTTATGG 9 11.8 ••••••••••• 1.5·10−10 340 HNRNPH1 Heterogeneous nuclear ribonucleoprotein H DA 5− 179048242 179046408 1834 AATTTTAGGT ACCTAAAGTT 10 13.6 ••••• ••••◦◦ 4.7·10−11 341 HNRNPH1 Heterogeneous nuclear ribonucleoprotein H AA trans 5− 179048036 179044933 3103 ACCTCTTTC GGAAGAGGT 9 15.8 ••••• ••••◦◦ 1.0·10−14 342 HNRNPH3 Heterogeneous nuclear ribonucleoprotein H3 AD exon 10+ 70097614 70097753 139 TTTAACACT GGTGTTAAA 9 12.6 ••◦••••••••• 2.6·10−6 −9

12 343 HNRNPK Heterogeneous nuclear ribonucleoprotein K AA trans 9− 86588888 86588314 574 TAGCTTTACCA TGGTAAAGTTA 11 17.2 •••••••••• 1.4·10 344 HNRNPK Heterogeneous nuclear ribonucleoprotein K DA intron 9− 86590376 86589504 872 TTCCCCATT AATGGGGAA 9 17.3 ••••••••••• 2.9·10−7 345 HNRNPL Heterogeneous nuclear ribonucleoprotein L AD exon 19− 39331199 39331127 72 GGGAGGGAG CTCCCTCTC 9 19.2 ••••••••• 4.1·10−12 346 HNRNPM Heterogeneous nuclear ribonucleoprotein M DA 19+ 8527465 8548041 20576 GAAATCAGGAAGG TCTTCCTGATTTC 13 22.1 •••••••••• 6.8·10−11 −1 347 HNRNPM Heterogeneous nuclear ribonucleoprotein M DD cis X 19+ 8530246 8530246 0 GGTGGGATG TATCCCACC 9 18.7 ••••••••••• 8.7·10 348 HNRNPM Heterogeneous nuclear ribonucleoprotein M AD 19+ 8527412 8530246 2834 TTTCTGGGC GCCCAGGAA 9 17.9 ••••••••••◦ 2.1·10−4 349 HNRNPM Heterogeneous nuclear ribonucleoprotein M AA trans 19+ 8528380 8530363 1983 GCTCTTCTG CAGGAGAGC 9 17 ••◦•••••••◦ 4.3·10−11 −1 350 HNRPDL N/A AA cis X 4− 83346820 83346820 0 TGGGTACAA TTGTACCCG 9 16.7 •••••••••••• 9.9·10 351 HOXA11 protein Hox-A11 DD cis 7− 27224054 27224054 0 TTTATATGC GCATATAAG 9 11.8 • • • • • • • • • ◦ 9.9·10−1 352 HOXB6 Homeobox protein Hox-B6 DD cis 17− 46681841 46681841 0 GGGGTGGGG CCCCACCTC 9 21.1 •••••••••• ◦ 6.7·10−9 353 HOXC6 Homeobox protein Hox-C4 AD 12+ 54422359 54448145 25786 AAAGGCAAAG CTTTGCTTTT 10 13.9 •••••••••• ◦ 4.9·10−6 354 HOXC6 Homeobox protein Hox-C4 DD trans 12+ 54411198 54448145 36947 GAGGGTGGG CCCACCCTC 9 22 • • • • • • • • • ◦ 2.2·10−13 355 HOXC6 Homeobox protein Hox-C4 DA 12+ 54422705 54447700 24995 CAATCACGC GTGTGATTG 9 14.7 •••••••••◦ ◦ 7.9·10−6 356 HOXC6 Homeobox protein Hox-C4 AD exon 12+ 54447700 54448145 445 CAGGGTCGCT AGCGACTCTG 10 20.3 ••••••••◦• ◦ 6.1·10−7 357 HOXD8 Homeobox protein Hox-D8 DD cis 2+ 176995671 176995671 0 AGGGGGAGA TCTCCCCCT 9 22.2 • • • • • • • • • ◦ 2.4·10−8 −6 358 HPN Serine protease hepsin AA cis X 19+ 35533356 35533356 0 CCCAGTCCC GGGACTGGG 9 22 ••••••••• 2.2·10 −2 359 HSF4 protein 4 isoform b AA cis X 16+ 67201726 67201726 0 GGCCAGTCC GGGCTGGCC 9 21.5 • • • • ◦ • • • • • 3.5·10 360 HSPG2 Basement membrane-specific heparan sulfate DD trans 1− 22190592 22150798 39794 GGGGCAGGG TCCTGCCCC 9 22.3 ◦ • • • • • • • • • 1.5·10−22 361 HUWE1 E3 ubiquitin-protein ligase HUWE1 AD X− 53591683 53586314 5369 CAAACTTGC GCAAGTTTG 9 14.6 ••••••••• 8.2·10−14 362 HUWE1 E3 ubiquitin-protein ligase HUWE1 AD X− 53713313 53589071 124242 TCTCCCCTC GAGGGGGGA 9 20.4 ••••••••• 2.7·10−12 363 HUWE1 E3 ubiquitin-protein ligase HUWE1 DD trans X− 53621458 53588716 32742 TAAGGATCA TGATTCTTA 9 12.7 •••••••••• ◦ 5.3·10−22 364 HUWE1 E3 ubiquitin-protein ligase HUWE1 DA X− 53589071 53587377 1694 CTCCCTCAT ATGAGGGAG 9 18.8 •••••••••• 1.1·10−11 365 HUWE1 E3 ubiquitin-protein ligase HUWE1 AD X− 53588885 53563340 25545 ATTCTCCAT ATGGAGAGT 9 15.4 ••••••◦••• ◦ 2.0·10−19 366 HUWE1 E3 ubiquitin-protein ligase HUWE1 AD X− 53589890 53578226 11664 CTCTGTTGT ACAGCAGAG 9 16.1 •••••◦•••• ◦ 8.8·10−18 367 HUWE1 E3 ubiquitin-protein ligase HUWE1 DD trans X− 53590706 53578226 12480 TTGCTCAGCTCT AGAGCTGAGCAG 12 24.8 •••••••••• ◦ 7.1·10−16 Supplementary Table 1: (continued)

368 IKZF2 Zinc finger protein Helios isoform 1 AD 2− 214014971 214014904 67 GGGAAAGAGAG TTCTCTTTCTC 11 17.4 • ◦ • • • • • • • • 8.8·10−8 369 IKZF2 Zinc finger protein Helios isoform 1 AA cis 2− 214014971 214014971 0 TTTCCTTCC GGAGGGAAA 9 15.9 •••••••••• 8.6·10−7 370 ILDR2 Immunoglobulin-like domain-containing receptor AA cis 1− 166904714 166904714 0 TTGTGGAGGG CCCTCCACAG 10 21.4 •••••••◦•• ◦ 3.0·10−13 371 ILF3 Interleukin enhancer-binding factor 3 isoform d AA trans 19+ 10795091 10795534 443 TTGTCTTGA TCAAGGCAA 9 14.5 •••••••••• ◦ 3.7·10−7 −2 372 ILF3 Interleukin enhancer-binding factor 3 isoform d AA cis X 19+ 10795091 10795091 0 GGAGCAGAGA TCTCTGCTCT 10 21.1 ••••••••••• 1.1·10 373 ILF3 Interleukin enhancer-binding factor 3 isoform d AA trans 19+ 10791021 10795534 4513 TGTTTTCCA TGGAAAGCA 9 14.8 •••••••••• ◦ 8.8·10−11 374 ILKAP Integrin-linked kinase-associated DA intron 2− 239098493 239096898 1595 CCCAGAGCAA TTGCTCTGGG 10 21.7 ••••••• ◦••◦ 1.8·10−25 375 IMPDH2 Inosine-5’-monophosphate dehydrogenase 2 DD trans 3− 49064119 49062091 2028 AGTACATCA TGATGTACT 9 15.5 • • ◦ • • • • • • • 1.7·10−18 376 INPP4B Type II inositol-3,4-bisphosphate 4-phosphatase AA cis 4− 142950067 142950067 0 AATGTAGAGTTG CAACTCTGCATT 12 19.4 ••••••••••• 2.1·10−5 377 INTS3 Integrator complex subunit 3 DA 1+ 153701260 153724754 23494 GGGAAGGGA TTCCTTCCC 9 18.1 ••••••••• 8.2·10−14 378 IPO13 -13 DD trans 1+ 44423830 44429993 6163 GAAACAGAT ATCTGTTTC 9 14.1 ••••••••• 1.6·10−7 379 IPO13 Importin-13 DD trans 1+ 44422987 44426934 3947 GCAGAGACC GGTCTCTGC 9 20 • • • • • ◦ • • • • 3.5·10−13 380 IQCH IQ domain-containing protein H isoform 1 DD cis 15+ 67681344 67681344 0 ATCAGTGAA TTTACTGAT 9 13.1 ••◦••••••••◦ 1.8·10−7 381 IQCH IQ domain-containing protein H isoform 1 DD trans 15+ 67665000 67681344 16344 AGCTGTTAAG TTTAACAGCT 10 15.6 ••••••• •◦•◦ 2.3·10−18 382 IQCH IQ domain-containing protein H isoform 1 DD cis 15+ 67786704 67786704 0 TGAGGTGTT AATACCTCA 9 15.4 ••••••••••• 1.2·10−4 383 IQCH IQ domain-containing protein H isoform 1 DD trans 15+ 67652223 67665771 13548 GGCAAGAGT ACTTTTGCC 9 15.9 •••••••••◦◦ 9.7·10−13 384 IQCH IQ domain-containing protein H isoform 1 DD trans 15+ 67652223 67665000 12777 TGACAGCTG CAGCTGTTA 9 16.3 • • • • • • • • • ◦ 3.3·10−18 385 IQCH IQ domain-containing protein H isoform 1 AA cis 15+ 67709268 67709268 0 CCACAAGCAGTTTT AAAATTGCTTGTGG 14 22.9 •••••••••••◦ 4.8·10−2 386 IQCH IQ domain-containing protein H isoform 1 AD exon 15+ 67786595 67786704 109 CATTTGTTT AAACAAGTG 9 11.1 ••••••••••• 2.4·10−7 387 IQCH IQ domain-containing protein H isoform 1 DA 15+ 67681344 67786595 105251 TTTCAGGGA TCCCTGAAG 9 17.1 ••••••••••• 9.2·10−8 388 IQCH IQ domain-containing protein H isoform 1 AA cis 15+ 67786595 67786595 0 ACAAATGAG CTCATTTGT 9 13.8 •••••••••◦◦ 1.8·10−1 −15

13 389 IQSEC2 N/A DD trans X− 53310677 53277902 32775 GCTCCCTTC GGAGGGAGC 9 19.4 •••••••••• 4.4·10 −13 390 IQSEC2 N/A AD exon X X− 53265014 53264964 50 GGGAGGGGC GCCTCTCCC 9 21.4 •◦•••••••• ◦ 3.0·10 −7 391 IQSEC2 N/A AA cis X X− 53265014 53265014 0 GGAGCCCAG CTGGGCTCC 9 22 •••••••◦•• ◦ 2.8·10 392 IQSEC2 N/A AA trans X− 53280356 53265014 15342 TCCCTTTCCC GGGAAAGGGA 10 21.9 ••••••••• 5.0·10−10 393 IQSEC2 N/A DD trans X− 53310677 53264964 45713 TCCCTTCCT AGGAGGGGA 9 19.5 • • ◦ • • • • • • • 1.9·10−11 394 IQSEC2 N/A AA trans X− 53308841 53265014 43827 CCCTTTTCCCC GGGGGAAAGGG 11 23.2 ••••••••• 1.5·10−8 395 IQSEC2 N/A DA X− 53321076 53268476 52600 GGGTGGGGG CCCCCACCC 9 24.1 •••••••••• 2.1·10−16 396 IVNS1ABP Influenza virus NS1A-binding protein AD exon 1− 185274775 185274667 108 GAGGTTACC GGTAACCTC 9 17.7 •••••••••• ◦ 5.3·10−15 397 JAG1 Protein jagged-1 precursor DD trans 20− 10626003 10625510 493 TCCAGGTGA TCACCTGGG 9 19 ••◦••••••• ◦ 1.0·10−22 398 KALRN isoform 1 DA 3+ 124114190 124210169 95979 AAATGCCTG TAGGCATTT 9 14.8 • • • • • • • • ◦ • 7.8·10−12 399 KAT5 Histone acetyltransferase KAT5 isoform 3 DA 11+ 65480305 65481063 758 GAGCGGCTGG CCAGCCGCTC 10 24.5 •••••••••• 4.5·10−10 400 KAT5 Histone acetyltransferase KAT5 isoform 3 DD trans 11+ 65479750 65480974 1224 GAGGTGGGT ACCCACCTT 9 19.8 • • • • ◦ • • • • • 3.6·10−4 401 KAT5 Histone acetyltransferase KAT5 isoform 3 DA 11+ 65480974 65482291 1317 AGGTGGAGG CCTCTACCT 9 18.5 ••••••••◦◦ • 1.2·10−16 402 KATNAL2 Katanin p60 ATPase-containing subunit A-like 2 DA intron 18+ 44589732 44593391 3659 TGATCATTT AAATGATCA 9 13 ••◦◦•••••••◦ 1.9·10−20 403 KCNC1 Potassium voltage-gated channel subfamily C DA intron 11+ 17801191 17803216 2025 GGGCAGGCAGG TCTGCCTGCCT 11 25.4 •••••••••• 2.0·10−11 −8 404 KCNMA1 Calcium-activated potassium channel subunit DD cis X 10− 78785203 78785203 0 GAGATTATA TATAATCTC 9 12.6 ••••••••◦• ◦ 8.0·10 405 KCNMA1 Calcium-activated potassium channel subunit DA 10− 78704530 78637651 66879 CAAGAGGGA TCCTTCTTG 9 15.9 • • • • • • • • • ◦ 3.4·10−10 406 KCNMA1 Calcium-activated potassium channel subunit AD 10− 78944674 78846245 98429 CTTCTTCCT AGGAGGAAG 9 15.9 • • • • • • • • ◦ • 2.6·10−20 407 KCNMA1 Calcium-activated potassium channel subunit DD trans 10− 78771724 78729731 41993 CCCCTCCCT GGGGAGGGG 9 23.1 ••◦•••••◦• • 4.6·10−21 408 KCNMA1 Calcium-activated potassium channel subunit DD trans 10− 78868238 78771724 96514 TGTTTCTTT AGAGAAACA 9 12.5 ••◦••••••• ◦ 3.4·10−13 409 KCP Kielin/chordin-like protein isoform 1 DA 7− 128534028 128532848 1180 TGTTGGCAG CTGCCAGCA 9 18.2 ••◦•••••••◦ 6.8·10−19 −7 410 KDM1A Lysine-specific histone demethylase 1A isoform AA cis X 1+ 23370919 23370919 0 TAGTTGGTG CGCCAACTA 9 15.8 ••••••••••◦◦ 2.7·10 411 KDM6A Lysine-specific demethylase 6A DD trans X+ 44919401 44941885 22484 GGGTTCTTT AAAGGACCC 9 15.5 •••••◦••◦• • 2.7·10−13 412 KIAA0913 Hypothetical protein LOC23053 DA 10+ 75549297 75556870 7573 GTGAGGCCCTC GAGGGCTTCAC 11 23.9 ••••••••◦• ◦ 4.7·10−17 413 KIAA0913 Hypothetical protein LOC23053 DD trans 10+ 75559952 75560517 565 GGGAGGTGGGG CCCCACCTTCC 11 25.7 •••••••••• 1.7·10−11 Supplementary Table 1: (continued)

414 KIAA0913 Hypothetical protein LOC23053 DD cis 10+ 75560517 75560517 0 GAGTTGAGG CCTCAGCTC 9 17.5 • ◦ • • • • • • • • 3.6·10−6 415 KIAA0913 Hypothetical protein LOC23053 DA 10+ 75556772 75560774 4002 GGGCAGGGGGG TCCCCCTGCCC 11 28.9 • • ◦ • • • • • • • 1.0·10−8 416 KIAA1409 Protein unc-79 homolog AA trans 14+ 93940593 94083467 142874 GAAGGAAAA TTTTCCTTT 9 12.7 • • • • • • • • • ◦ 1.1·10−11 417 KIAA1409 Protein unc-79 homolog AA cis 14+ 93940593 93940593 0 GCACAGGGAA TTTCCTGTGC 10 18.9 • • ◦ • • • • • • • 9.9·10−1 418 KIAA1468 Hypothetical protein LOC57614 AA trans 18+ 59888269 59947592 59323 TTTCTTGGTT AACCAAGAAA 10 15.7 ••◦••••••• ◦ 6.2·10−6 419 KIAA2026 Putative uncharacterized protein AA cis 9− 5954095 5954095 0 CTTTCAAGG TCTTGAAAG 9 12.9 • • • • • • • • • ◦ 3.5·10−7 420 KIF1B -like protein KIF1B isoform b AA cis 1+ 10342457 10342457 0 GATTTTCAGA TCTGAGAATC 10 15.3 • • • • • • • • • ◦ 2.2·10−6 −18 421 KIF21A Kinesin-like protein KIF21A isoform 1 DA intron X 12− 39724547 39724064 483 GAATAGATGCT GGCATCTATTC 11 18.9 ••••••••••• 7.1·10 422 KLHL29 Kelch-like protein 29 AD exon 2+ 23907268 23907407 139 GGGAACCTG CAGGTTCCT 9 18.4 •••••••••◦◦ 7.3·10−7 423 KPNA3 Importin subunit alpha-3 DA intron 13− 50296612 50296260 352 CTATGTTTCCTC GAGGAAACATAG 12 20.8 •••••••••• 3.0·10−15 424 KPNB1 Importin subunit beta-1 DD cis 17+ 45727650 45727650 0 GGGGGAGGG TCCTCCCCC 9 22.5 ••••••◦••• ◦ 1.9·10−11 425 KPNB1 Importin subunit beta-1 DD trans 17+ 45727650 45727810 160 GGGGGAGGGG CCCCTCCCCC 10 27.6 ••••••◦••• • 5.2·10−15 426 L3MBTL1 Lethal(3)malignant brain tumor-like protein DA 20+ 42144055 42161412 17357 GGGCAGTGGG CCCACTGTCC 10 22.4 • • ◦ • • • • • • • 5.5·10−22 427 LACE1 Lactation elevated protein 1 DA intron 6+ 108798138 108798394 256 ATTTTGTCT AGACAAGAT 9 12.7 ••◦••••••• • 9.9·10−1 428 LAMA1 Laminin subunit alpha-1 precursor DD trans 18− 7032982 6992559 40423 CTTCTCTCTT AAGAGAGGAG 10 16.9 •••••••◦••• 2.1·10−29 429 LDB1 LIM domain-binding protein 1 isoform 3 DD trans 10− 103870825 103868785 2040 GGGATGCTT AAGCATCTC 9 15.6 ◦•••••••••◦ 7.1·10−20 430 LOC641518 N/A AD exon 4+ 109094574 109094675 101 TTTTTCCCT AGGGAGAAA 9 14.8 • • • • • • • • • ◦ 2.0·10−12 431 LPHN2 Latrophilin-2 precursor AD 1+ 82408652 82432293 23641 TTTTGTCTT AAGACAAGA 9 12.5 ••◦••••••• ◦ 1.6·10−20 432 LRP1 N/A DD trans 12+ 57554898 57585295 30397 GTGTGTCCA TGGACATAC 9 16.7 • • • • • • • • ◦ • 7.8·10−25 433 LRP1 N/A DD trans 12+ 57550703 57596320 45617 GCGGGAGGG CCCTCCTGC 9 21.3 •••••••••• 5.4·10−22 434 LRP1 N/A DA 12+ 57522814 57602493 79679 GGGAGGGGG CCTCCTCCC 9 21.3 • • • • ◦ • • • • • 1.0·10−17 −14

14 435 LRP1 N/A DD trans 12+ 57522814 57578773 55959 GGGAAGGGA TTCCTTCCC 9 18.1 ••••••••• 8.4·10 −1 436 LRP12 Low-density lipoprotein receptor-related protein DD cis X 8− 105544134 105544134 0 GTAAGTCAT ATGACTTAT 9 13.5 •••••••••• ◦ 2.5·10 437 LRP1B Low-density lipoprotein receptor-related protein DA 2− 141215031 141143578 71453 TTTCCATGA TCATGGAAA 9 15.2 • • ◦ • • • • • • • 1.8·10−17 438 LRPPRC Leucine-rich PPR motif-containing protein, AD 2− 44175657 44132830 42827 CGGTAATTT AAATTACTG 9 10.8 •••••••••• 5.2·10−1 439 LRPPRC Leucine-rich PPR motif-containing protein, AD exon 2− 44132919 44132830 89 CAGTAGTTT AAATTACTG 9 11.5 ••••••••••• 9.5·10−1 440 LRPPRC Leucine-rich PPR motif-containing protein, AA trans 2− 44171033 44132919 38114 CGTTTAGAA TTCTAAATG 9 11.3 • • • • • • • • • ◦ 9.9·10−1 441 LRPPRC Leucine-rich PPR motif-containing protein, DA 2− 44175550 44132919 42631 CTGACATGT GCATGTCAG 9 16.6 ••••••••••• 5.9·10−4 442 LRPPRC Leucine-rich PPR motif-containing protein, AA trans 2− 44175657 44171033 4624 ATTTTAGTG CACTAGAAT 9 11.6 ••••• •••••◦ 2.6·10−5 443 LRRC16B Leucine-rich repeat-containing protein 16B DD trans 14+ 24523012 24528195 5183 GGGGGAGGAG CTCCTCCTCC 10 22.5 •••••••••• ◦ 1.0·10−22 444 LRRC7 Leucine-rich repeat-containing protein 7 DD trans 1+ 70501915 70505476 3561 TGCATGTGC GCACATGTA 9 16.5 • • • • • • • ◦ • • 2.0·10−15 445 MACF1 - cross-linking factor 1 isoform AA trans 1+ 39902146 39907818 5672 CATTTCATT AATGAAATG 9 11.5 ••◦•◦•••••• 2.9·10−15 446 MACF1 Microtubule-actin cross-linking factor 1 isoform AA trans 1+ 39908083 39913363 5280 TCTGGGAGA TTTCCCAGA 9 17.5 •••••• •••◦◦ 5.7·10−25 447 MACF1 Microtubule-actin cross-linking factor 1 isoform AA cis 1+ 39902146 39902146 0 TGGAATGTG CACATTTCA 9 13.3 ••◦•••••••• 1.6·10−1 448 MACROD2 MACRO domain-containing protein 2 isoform 1 AD exon 20+ 15913920 15913983 63 TTCATCTCT AGAGGTGAA 9 14.9 ••••••••◦• ◦ 2.2·10−20 449 MADD MAP kinase-activating death domain protein AA trans 11+ 47331057 47350208 19151 CAGGGTCCC GGGACCCTG 9 22 ••••••••◦• ◦ 2.0·10−19 450 MAP2K5 Dual specificity mitogen-activated protein AA trans 15+ 67878227 67985855 107628 GAGCAAATT AATTTGTTC 9 11.4 ••••• •••••◦ 3.3·10−4 451 MAP2K5 Dual specificity mitogen-activated protein DA 15+ 67878268 67893022 14754 GAAATGTCAA TTGACATTTC 10 15 •••••••••••◦ 3.6·10−7 452 MAP2K5 Dual specificity mitogen-activated protein AD 15+ 67878227 67885312 7085 TCTGCTAAT ATTGGCAGA 9 15.1 ••••◦••••••◦ 2.3·10−16 453 MAP2K5 Dual specificity mitogen-activated protein AA trans 15+ 68040568 68040906 338 AATGCAATAA TTATTGCATT 10 13.8 •••••••••••◦ 2.9·10−4 454 MAP2K5 Dual specificity mitogen-activated protein AA trans 15+ 67842371 68020253 177882 TTTGTTTAG CTAGACAAA 9 11.4 • • • • • • • • • ◦ 7.3·10−11 455 MAP2K5 Dual specificity mitogen-activated protein AA trans 15+ 67879183 67893022 13839 GCAACAAGC GCTTGTTGT 9 16.2 •◦◦••••••••◦ 1.6·10−13 456 MAP2K5 Dual specificity mitogen-activated protein DA 15+ 67873161 67985855 112694 GAGCAAATT AATTTGTTC 9 11.4 ••••• ••••◦◦ 1.3·10−8 457 MAP2K5 Dual specificity mitogen-activated protein DA 15+ 67878268 68020253 141985 ATGGATTTG CAAATCTAT 9 11.6 •••••••••••◦ 1.6·10−12 458 MAP2K5 Dual specificity mitogen-activated protein DA 15+ 67873161 68040568 167407 AAATGCACA TGTGTATTT 9 12.8 ••••◦••◦•••◦ 4.2·10−6 459 MAP2K5 Dual specificity mitogen-activated protein AA trans 15+ 67893022 68040568 147546 GCAAATGTTG TAACATTTGT 10 13.7 ◦••••••••••◦ 5.9·10−7 Supplementary Table 1: (continued)

460 MAP2K5 Dual specificity mitogen-activated protein AD 15+ 67879183 68020283 141100 ACCTTCATA TATGAAGGT 9 15.4 •••••••◦◦••◦ 1.4·10−16 461 MAP2K5 Dual specificity mitogen-activated protein AD 15+ 67873091 68020283 147192 TTCATACAT ATGTATGAA 9 13.2 ••◦•••••••• 5.4·10−11 462 MAP2K5 Dual specificity mitogen-activated protein AA trans 15+ 67893022 68040906 147884 GACAGCAAAC GTTTGCTGTT 10 17.2 ••••••••••◦◦ 1.0·10−6 463 MAP2K5 Dual specificity mitogen-activated protein AA cis 15+ 67879183 67879183 0 AATTAACCT AGGTTAATT 9 12.7 ••◦•••••◦••• 5.2·10−12 464 MAP2K5 Dual specificity mitogen-activated protein AD 15+ 68020253 68040595 20342 GCATGCAAA TTTGCATGC 9 16 ••◦•••••••◦◦ 2.9·10−8 465 MAP2K5 Dual specificity mitogen-activated protein DA 15+ 67873161 68040906 167745 TAATCAACAAT GTTGTTGATTA 11 15.3 •••••••••••◦ 2.7·10−9 466 MAP2K5 Dual specificity mitogen-activated protein DD trans 15+ 68040595 68040939 344 GTAAGCTTT AAAGCTTAT 9 13 •••••••••••• 1.0·10−4 467 MAP2K5 Dual specificity mitogen-activated protein AD 15+ 67985855 68040939 55084 TTTCCACAT GTGTGGAAA 9 15.3 ••••• •••••◦ 1.4·10−7 468 MAP2K5 Dual specificity mitogen-activated protein AA trans 15+ 67873091 68040568 167477 ATTACTGAG CTCAGTGAT 9 14.3 ••••••••••• 2.7·10−7 469 MAP2K5 Dual specificity mitogen-activated protein AD 15+ 67878227 68020283 142056 CTTTTCAAT ATTGAAAAG 9 11.3 ••◦••••••••◦ 1.5·10−7 470 MAP2K5 Dual specificity mitogen-activated protein AD exon 15+ 68040568 68040595 27 TGTATTTTC GAAAATGCA 9 11.8 •••••••••••◦ 9.9·10−1 471 MAP2K6 Dual specificity mitogen-activated protein DD cis 17+ 67411141 67411141 0 AAAAATGCA TGCATTTTT 9 12.3 •••••••••• ◦ 9.3·10−6 472 MBNL1 Muscleblind-like protein 1 isoform e DA 3+ 152164546 152173330 8784 TGGCATGTA TACATGCCA 9 17.6 ••◦••••••• ◦ 6.7·10−6 473 MBNL1 Muscleblind-like protein 1 isoform e AA trans 3+ 152164492 152173330 8838 CCATCATGT GCATGATGG 9 16.7 ••••••••••• 9.1·10−1 474 MBNL1 Muscleblind-like protein 1 isoform e AA trans 3+ 152174055 152175918 1863 CTTCTGTATG CATGCAGAAG 10 16.3 ••••••••◦• • 2.0·10−4 475 MBNL2 Muscleblind-like protein 2 isoform 3 DD trans 13+ 98017425 98018807 1382 TTTAGAGTT AACTCTAAA 9 12.8 •••◦•••••• ◦ 3.5·10−9 476 MCTP1 Multiple C2 and transmembrane domain-containing DA 5− 94206576 94114868 91708 TTCTGTCAT ATGACAGAA 9 15.3 •••••••••◦ ◦ 6.7·10−11 477 MCTP1 Multiple C2 and transmembrane domain-containing AD 5− 94206678 94114814 91864 TGTCATGTC GACATGACA 9 16.6 ••••••◦••• • 1.7·10−5 478 MCTP1 Multiple C2 and transmembrane domain-containing DA 5− 94207019 94114868 92151 TCTGTCATTT AAATGACAGA 10 16.2 •••••••••◦ ◦ 2.6·10−14 479 MCTP1 Multiple C2 and transmembrane domain-containing AA trans 5− 94206678 94043272 163406 GCAGCTGGG CTCAGCTGC 9 18.8 ••◦•• •••••◦ 1.0·10−10 480 MCTP1 Multiple C2 and transmembrane domain-containing DA 5− 94206576 94043272 163304 AGAGTTCAG CTGAACTCT 9 16.3 ••◦•• •••••• 1.0·10−12 −14 15 481 MDM4 N/A AD exon X 1+ 204506557 204506625 68 CAGGGAAGG CCTTCTCTG 9 16.5 •••••••••••◦ 6.5·10 −4 482 MDM4 N/A DD cis X 1+ 204506625 204506625 0 TGGACTCCCAAGA TCTTGGGAGTTCA 13 25.7 •••••••••••• 1.4·10 483 MECOM MDS1 and EVI1 complex protein EVI1 isoform DD cis 3− 168830574 168830574 0 TAGGATTTCCT AGGAAATTCTA 11 16.9 ••◦•••••••◦◦ 5.5·10−7 484 MECOM MDS1 and EVI1 complex locus protein EVI1 isoform AD 3− 168834527 168830574 3953 TTTCTGTGT ACACAGGAA 9 14.4 ••◦•••••••◦◦ 7.0·10−15 −5 485 MECP2 Methyl-CpG-binding protein 2 isoform 2 DD cis X X− 153357641 153357641 0 TTCCTTTTTTT AAAAAAAGGAA 11 14.1 •••••••••• 2.5·10 486 MED12 Mediator of RNA polymerase II transcription AD X+ 70345885 70349279 3394 TCTCTCCCTCCCT GGGGAGGGAGAGA 13 31.2 ••••••••• 1.0·10−7 −9 487 MED23 Mediator of RNA polymerase II transcription DA intron X 6− 131937046 131936481 565 GCAAAACAGT ACTGTTTTGT 10 15.9 ••••••••••• 3.7·10 −1 488 MEF2A Myocyte-specific enhancer factor 2A isoform 2 DD cis X 15+ 100211659 100211659 0 TCCTTTTTGTT AACAAGAAGGA 11 16.7 ••••••••••◦◦ 9.9·10 489 MEF2C Myocyte-specific enhancer factor 2C isoform 4 DD trans 5− 88057085 88056804 281 ATCAGCAGGC GTCTGCTGAT 10 19.3 •••••••••••• 1.5·10−13 490 MEF2C Myocyte-specific enhancer factor 2C isoform 4 DA 5− 88178771 88044934 133837 CTGATATTT AAATGTCAG 9 11.9 •••••••◦••◦ 3.0·10−23 491 MEF2C Myocyte-specific enhancer factor 2C isoform 4 AA trans 5− 88057145 88018646 38499 AGGTTTGAACTTT AGAGTTCAAATCT 13 18.4 ••••••••••◦◦ 3.1·10−13 492 MEIS1 Homeobox protein Meis1 AA trans 2+ 66666974 66667693 719 GGGGAGGGGGA TCCCTCTCCCC 11 27 ••◦•••••◦• • 5.2·10−19 493 MEIS2 Homeobox protein Meis2 isoform a AA cis 15− 37329160 37329160 0 TGAAAGAGA TTTCTTTCA 9 12.7 •••••••◦•• ◦ 2.9·10−7 494 MET Hepatocyte growth factor receptor isoform b DD trans 7+ 116415165 116435845 20680 AGCATTTTA TAAAATGCT 9 12.7 ••◦••••••• ◦ 7.5·10−20 495 MGEA5 Bifunctional protein NCOAT isoform b AD exon 10− 103553755 103553669 86 TTTCTCGTAA TTATGAGAAA 10 13.7 •••••••••••◦ 8.8·10−9 496 MGEA5 Bifunctional protein NCOAT isoform b DD cis 10− 103553669 103553669 0 ACTGAATTGA TCAATTTAGT 10 14 •••••••••••◦ 9.7·10−1 497 MICAL3 Protein MICAL-3 isoform 1 DA 22− 18370088 18305826 64262 AGGAAAAGG CCTTTTCTT 9 13.2 ••••• •◦•••◦ 1.6·10−27 498 MIPOL1 Mirror-image polydactyly gene 1 protein DD cis 14+ 37777294 37777294 0 ATATCTTAG CTAAGATGT 9 12.3 ••••••••••• 8.2·10−1 499 MIPOL1 Mirror-image polydactyly gene 1 protein AA trans 14+ 37716307 37777260 60953 GAACATATT AATATGTTC 9 12 • • • • • • • • • ◦ 6.2·10−3 500 MIR1231 navigator 1 isoform 1 AA trans 1+ 201757595 201759816 2221 CCCTGCCTC GAGGTAGGG 9 20 •••••••••• ◦ 1.0·10−17 501 MLL2 Histone-lysine N-methyltransferase MLL2 AA trans 12− 49446492 49436428 10064 CCTCTGCAG CTGCAGAGG 9 19.6 ••••••••••◦ 2.6·10−23 502 MLL4 Histone-lysine N-methyltransferase MLL4 AD 19+ 36218598 36221517 2919 GTGCTCCAG CTGGAGCAC 9 19.7 • • • • ◦ • • • • • 8.0·10−18 503 MRRF Ribosome-recycling factor, mitochondrial isoform AA cis 9+ 125054027 125054027 0 ACTGGTAAC GTTGCCAGT 9 16.3 •••••••••• 9.9·10−1 504 MSI1 RNA-binding protein Musashi homolog 1 AD 12− 120806076 120796807 9269 GGGGGGGGGGG CCCCCTCCCCC 11 30 • • • • • • • • • ◦ 1.5·10−12 505 MSI1 RNA-binding protein Musashi homolog 1 AD 12− 120800938 120794704 6234 GACTCAGAT GTCTGAGTC 9 17.1 • • • • • • • • • ◦ 1.7·10−16 Supplementary Table 1: (continued)

506 MSI2 RNA-binding protein Musashi homolog 2 isoform b DA intron 17+ 55729522 55752332 22810 CCAGGCATGC GCATGCCTGG 10 22.9 •••••••••• ◦ 5.9·10−13 507 MSL1 Male-specific lethal 1 homolog AA cis 17+ 38279537 38279537 0 GCCACCGCC GGTGGTGGC 9 21.5 ••◦•••••••◦◦ 3.7·10−6 508 MSL1 Male-specific lethal 1 homolog AD 17+ 38279537 38285880 6343 ACCGCCACC GGTGGCGGT 9 22.2 •••••••◦••◦◦ 2.5·10−10 509 MST1 Hepatocyte growth factor-like protein precursor AD exon 3− 49724911 49724796 115 CTCTTCCAG CTGGAAGAG 9 17.4 •••••••◦••◦◦ 3.1·10−30 510 MTDH Protein LYRIC DD cis 8+ 98699833 98699833 0 GTATATTAG CTGATATAC 9 11.4 ••••••••◦•◦◦ 5.7·10−13 511 MTMR3 Myotubularin-related protein 3 isoform b DA 22+ 30279348 30419445 140097 GAGGAGGGG CCCCTCCTT 9 21.1 •••••••••• 2.2·10−16 512 MYCBP2 Probable E3 ubiquitin-protein ligase MYCBP2 AD exon 13− 77807398 77807290 108 TTTCTCCTCAG CTGAGGAGAAA 11 20.7 ••••• ••••◦◦ 1.4·10−15 513 MYCBP2 Probable E3 ubiquitin-protein ligase MYCBP2 DA 13− 77713330 77699603 13727 AATTAAGGC GCCTTAATT 9 13.9 ••••• ••••◦◦ 2.6·10−21 514 MYH1 -1 DD trans 17− 10408479 10400603 7876 TCTTCTGCA TGCAGAAGG 9 16.6 ••••◦•••••◦ 7.5·10−25 515 MYH3 Myosin-3 DD trans 17− 10550679 10542614 8065 TTCCAGCTG CAGCTGGAA 9 18.4 ••••••◦•••◦◦ 2.6·10−28 516 MYH7B Myosin-7B AD 20+ 33565434 33588696 23262 TTGTGTCCTGT GCAGGACACAA 11 21.9 • • • • • • • • • ◦ 1.1·10−14 517 MYH8 Myosin-8 DA 17− 10322203 10296318 25885 CTCTTCTGT GCAGAAGAG 9 16.6 •••••••••• ◦ 3.8·10−23 518 MYH8 Myosin-8 DA 17− 10318788 10315836 2952 GGCCTTTGG CCAAAGGCC 9 19.3 •••••••••• ◦ 7.7·10−24 519 MYH8 Myosin-8 DA 17− 10322203 10304508 17695 CCTCTTCTG CAGAGGAGG 9 17.1 •••••••◦••◦◦ 1.4·10−24 520 MYL6B 6B AA trans 12+ 56547656 56548596 940 GCCAACTGGC GCCAGTTGGT 10 21.9 ••••••••••◦ 2.4·10−15 521 MYNN Myoneurin isoform B AA trans 3+ 169496671 169501264 4593 AGATGGAAGA TTTTCCATCT 10 16.2 ••◦•• •••••◦ 5.7·10−12 522 MYO15A Myosin-XV DD trans 17+ 18046933 18058539 11606 GTGGGGCAC GTGTCCCAC 9 19.2 • • • • • • • • • ◦ 1.4·10−19 523 MYOF Myoferlin isoform a AA cis 10− 95070400 95070400 0 GTTTTACAA TTGTGAAAC 9 11.5 ••••••◦••• ◦ 6.1·10−10 524 NBLA00301 N/A DD cis 4+ 174452229 174452229 0 GTTTTTATG CATAAAAGC 9 10.3 • • • ◦ • • • • • • 5.6·10−1 525 NCOA5 coactivator 5 DD cis 20− 44708025 44708025 0 AGTTGGGCT AGCCCAGCT 9 19.4 •••••••••• ◦ 3.2·10−5 526 NDST2 Bifunctional heparan sulfate AD 10− 75563774 75562729 1045 CTCTCCCAT GTGGGAGAG 9 19.1 ••◦•••••••◦ 9.0·10−24 −22

16 527 NEB Nebulin isoform 2 DA 2− 152551035 152359399 191636 ACAAGAAAG CTTTCTTGT 9 13.6 • • • • • • • • • ◦ 5.0·10 528 NEB Nebulin isoform 2 DA 2− 152544139 152359399 184740 ACAAGAAAG CTTTCTTGT 9 13.6 • • • • • • • • • ◦ 1.5·10−21 −7 529 NFAT5 Nuclear factor of activated T-cells 5 isoform b AA cis X 16+ 69680419 69680419 0 CTGGAATAA TTATTCCAG 9 14.1 ••••••••••• 4.1·10 −6 530 NFIB Nuclear factor 1 B-type isoform 2 DD cis X 9− 14116206 14116206 0 AAATGAGAAAT ATTTCTCATTT 11 14.8 •••••••••• ◦ 2.2·10 531 NFIB Nuclear factor 1 B-type isoform 2 DA 9− 14179725 14113080 66645 GGAGAACAAAG TTTTGTTCTTC 11 14.9 •••••••••• 1.1·10−10 532 NFYC Nuclear transcription factor Y subunit gamma DA 1+ 41157539 41236380 78841 GGGGGAGGGGC GCCCCTCTCCC 11 28 •••••••••• 4.3·10−16 533 NIPBL Nipped-B-like protein isoform B DD cis 5+ 37064080 37064080 0 GTATTACGT ATGTAATAC 9 11.8 ••◦••••••• ◦ 4.1·10−1 534 NIPBL Nipped-B-like protein isoform B DD trans 5+ 36877280 37064080 186800 CTCCTCCTC GAGGAGGAG 9 20.1 ••••••••••• 1.4·10−6 535 NKTR NK-tumor recognition protein DA intron 3+ 42663008 42672037 9029 ACAGAGAAG CTTCTTTGT 9 13.7 •••◦•••••• ◦ 4.5·10−19 −7 536 NLGN3 Neuroligin-3 isoform 2 DA intron X X+ 70368755 70373326 4571 AGAGAGAGAG TTCTCTCTCT 10 18.6 • • • • • • • • • ◦ 4.2·10 537 NLGN3 Neuroligin-3 isoform 2 AD X+ 70367399 70368755 1356 TCCCTCTTTC GAGAGAGGGA 10 19.9 • • • • • • • • • ◦ 2.1·10−16 −7 538 NLGN3 Neuroligin-3 isoform 2 AD exon X X+ 70373326 70373386 60 TCTCCCCGT ATGGGGAGA 9 19.6 •••••••••• ◦ 7.1·10 539 NLGN3 Neuroligin-3 isoform 2 AA trans X+ 70368695 70373326 4631 GGGACAGGC GCCTGTCCT 9 20.9 • • • • • ◦ • • • • 4.7·10−4 540 NOL4 Nucleolar protein 4 isoform 1 DA 18− 31708812 31537481 171331 TAGCTTCTT AGGAAGCTA 9 14.9 • • • • • • • ◦ • • 9.4·10−6 541 NOP56 Nucleolar protein 56 AD 20+ 2636240 2636680 440 ATGGGTCAG CTGACCTAT 9 16.3 • • • • • • • • • ◦ 4.8·10−12 542 NOTCH4 Neurogenic locus notch homolog protein 4 DA 6− 3661451 3658236 3215 GAGGAGGGA TCTCTCCTC 9 18.3 • • • • • • • • ◦ • 1.3·10−20 543 NPR2 Atrial natriuretic peptide receptor 2 precursor DD trans 9+ 35801760 35809244 7484 CTTTCATCC GGGTGAAAG 9 14.6 • • • • • • • • • ◦ 3.9·10−14 544 NR2E1 Nuclear receptor subfamily 2 group E member 1 AD exon 6+ 108501526 108501623 97 GCATTTAAA TTTAAATGC 9 11.5 •••••••◦◦• • 1.5·10−4 545 NR2E1 Nuclear receptor subfamily 2 group E member 1 AA trans 6+ 108501526 108502010 484 TATTGTATGA TCATACAATA 10 14.5 ••••••••◦• ◦ 2.8·10−9 546 NR4A2 Nuclear receptor subfamily 4 group A member 2 AA trans 2− 157183432 157182840 592 AGAGAGAGG TCTCTCTCT 9 17.1 •••••••••• ◦ 6.2·10−6 547 NR4A2 Nuclear receptor subfamily 4 group A member 2 DA intron 2− 157183229 157182840 389 GAGAAAAAG CTTTTTCTC 9 12.6 •••••••••• 1.6·10−10 548 NRBP1 Nuclear receptor-binding protein AD exon 2+ 27657999 27658094 95 CCCCTGCCC GGGCAGGGG 9 24.1 •••••••••• ◦ 1.0·10−10 549 NRG2 Pro-neuregulin-2, membrane-bound isoform isoform DA 5− 139245133 139244758 375 AGGGCCAGG CCTGGCTCT 9 19.9 • • • • • • • • • ◦ 2.9·10−8 550 NRXN1 Neurexin-1-beta isoform alpha2 precursor AA cis 2− 50280728 50280728 0 AGCAATGAA TTTATTGCT 9 12.8 •••••••••• 2.5·10−2 551 NRXN1 Neurexin-1-beta isoform alpha2 precursor AA trans 2− 50755789 50282182 473607 TTTTATTGG CCAATGAAA 9 11.5 •••••••••• 9.8·10−6 Supplementary Table 1: (continued)

−1 552 NRXN1 Neurexin-1-beta isoform alpha2 precursor AD exon X 2− 50848387 50848363 24 TACTAACCG CGGTTGGTA 9 15.4 •••••◦◦••• • 9.0·10 553 NRXN1 Neurexin-1-beta isoform alpha2 precursor AD exon 2− 50755789 50755762 27 GGTGGACTG CAGTCCATC 9 17.1 •••••••••• ◦ 1.2·10−8 554 NRXN1 Neurexin-1-beta isoform alpha2 precursor AA trans 2− 50282182 50280728 1454 ACAGATTTT AAGATCTGT 9 12.7 • ◦ • • • • • • • • 4.3·10−5 555 NRXN1 Neurexin-1-beta isoform alpha2 precursor DA 2− 50848363 50755789 92574 CTGTAGACATC GATGTCTGCAG 11 20 ••••••••••• 5.0·10−7 556 NRXN1 Neurexin-1-beta isoform alpha2 precursor AA trans 2− 50733755 50282182 451573 TCTGTGAGG CCTTACAGA 9 16.5 •••••••••• 6.2·10−5 557 NRXN2 Neurexin-2-beta isoform alpha-2 precursor AD 11− 64457948 64427803 30145 GCTTCTCCAG CTGGAGAAGC 10 20.8 •••••••••• 1.6·10−15 558 NRXN2 Neurexin-2-beta isoform alpha-2 precursor AD 11− 64436076 64421167 14909 CCTCCCTCCT GGGAGGGAGG 10 24.3 ••••••••• 5.7·10−14 559 NRXN2 Neurexin-2-beta isoform alpha-2 precursor DD trans 11− 64397873 64387765 10108 CGGGGCGGGG CCCTGCCCCG 10 25.8 ••••••••• 8.0·10−16 560 NRXN2 Neurexin-2-beta isoform alpha-2 precursor AD 11− 64444509 64421167 23342 CTCCTCCCC GGGGAGGGG 9 21.3 •••••••••• 2.8·10−13 561 NRXN2 Neurexin-2-beta isoform alpha-2 precursor DD trans 11− 64421167 64387765 33402 GGGGAGGGG CCCCTCCCC 9 24.3 •••••••••• 1.2·10−15 −11 562 NRXN2 Neurexin-2-beta isoform alpha-2 precursor AD exon X 11− 64421194 64421167 27 CCCCTCCCT GGGGAGGGG 9 23.1 • • • • • • • ◦ • • 1.3·10 563 NRXN2 Neurexin-2-beta isoform alpha-2 precursor DA 11− 64421167 64418110 3057 GTGGGGAGG CCTCCTCAC 9 19 ••••••••• 1.0·10−14 564 NRXN2 Neurexin-2-beta isoform alpha-2 precursor DD cis 11− 64387765 64387765 0 CCCCCCTCCC GGGAGGGGGG 10 27.6 • • • • • • • ◦ • • 1.8·10−7 565 NRXN2 Neurexin-2-beta isoform alpha-2 precursor DD trans 11− 64460318 64421167 39151 CCCCTCCTC GGGGAGGGG 9 21.3 ••••••••• 1.6·10−13 566 NT5C2 Cytosolic purine 5’-nucleotidase DD trans 10− 104860991 104860801 190 AGAGACCTAC GTAGGTCTTT 10 17.5 •••••••••• ◦ 1.8·10−14 −4 567 NTNG1 Netrin-G1 isoform 3 DD cis X 1+ 107963765 107963765 0 GATTCATACAGTG CACTGTATGAATC 13 22 ••••••••••• 9.9·10 568 NTNG1 Netrin-G1 isoform 3 AD 1+ 107973371 107979421 6050 TTTCTGTTCT AGAGCAGAAA 10 16 ••••••••◦• ◦ 5.4·10−16 569 NTRK1 High affinity nerve growth factor receptor DA 1+ 156838041 156841414 3373 GGGAGAGGG CCCTCTCTC 9 19.2 • • ◦ • • • • • • • 4.5·10−21 −24 570 NUMB Protein numb homolog isoform 4 AD exon X 14− 73783130 73783097 33 TAACTCTTT AAGGAGTTA 9 12.5 ••◦•••••••◦◦ 8.6·10 −9 571 NUP98 Nuclear pore complex protein Nup98-Nup96 isoform DD cis X 11− 3781768 3781768 0 ACTTTAGGA TCTTAAAGT 9 12.5 ••••••••••◦◦ 1.9·10 572 ODZ2 -2 DD trans 5+ 167553944 167638759 84815 AGGCAAACG CGTTTGCTT 9 14.6 ••◦••••••• • 1.0·10−9 −17

17 573 OGT UDP-N-acetylglucosamine–peptide DA X+ 70776955 70782979 6024 AGGGAATAT ATGTTCCCT 9 15.5 • • • • • ◦ • • • • 7.8·10 574 OLA1 Obg-like ATPase 1 isoform 1 AA cis 2− 174943818 174943818 0 GAAAAGAAA TTTCTTTTC 9 11.4 ••••◦••••• ◦ 9.2·10−9 575 OLA1 Obg-like ATPase 1 isoform 1 AD exon 2− 174946792 174946651 141 AATGAATGT GCATTCATT 9 13.1 ••••••••••• 9.9·10−1 576 OPA1 -like 120 kDa protein, mitochondrial AD 3+ 193335572 193361233 25661 TTTTGCTGA TCAGCAAAG 9 14.5 • • • • • • • • • ◦ 1.1·10−14 −10 577 OSR2 Protein odd-skipped-related 2 isoform a AA cis X 8+ 99963746 99963746 0 GGTGTGAAG CTTCACATC 9 14.7 •••••••••◦ ◦ 4.9·10 578 PABPC4 Polyadenylate-binding protein 4 isoform 2 DA 1− 40036905 40029413 7492 GGCCCCACC GGTGGGGCT 9 23 •••••••◦••◦ 6.1·10−8 −10 579 PAPD5 PAP-associated domain-containing protein 5 DA intron X 16+ 50258905 50259149 244 ACGTTTTCCAA TTGGAAAATGT 11 16.4 •••••••••• ◦ 1.8·10 −5 580 PATZ1 POZ-, AT hook-, and zinc finger-containing AA cis X 22− 31737669 31737669 0 AGAGGGCAG CTGCCCTTT 9 18.2 • • • • ◦ • • • • • 1.3·10 581 PAX2 Paired box protein Pax-2 isoform b DA 10+ 102541122 102568866 27744 GGAGGAGGG TCCTCCTCC 9 20.4 ••••••••• 6.1·10−9 582 PCBP2 Poly(rC)-binding protein 2 isoform e AD 12+ 53858543 53861627 3084 AGCTCCTTT AGAGGAGCT 9 17.3 ••••••••• 3.6·10−5 −2 583 PCBP2 Poly(rC)-binding protein 2 isoform e AD exon X 12+ 53858543 53858636 93 TGGAGACTGAA TTCAGTCTCCA 11 22 ••••••••• 1.5·10 584 PCBP2 Poly(rC)-binding protein 2 isoform e AD 12+ 53849244 53858636 9392 GTTGGCAGT ACTGCCAAC 9 18.3 ••••••••• 3.5·10−8 585 PCBP2 Poly(rC)-binding protein 2 isoform e DA 12+ 53858636 53862560 3924 AGTCTCCAA TTGGAGGCT 9 16.9 ••••••••• 1.0·10−5 586 PCBP2 Poly(rC)-binding protein 2 isoform e DA 12+ 53849154 53858543 9389 AGAAAGGAG CTCCTTTTT 9 13.6 ••••••••• 1.7·10−9 587 PCBP3 Poly(rC)-binding protein 3 isoform 2 AA cis 21+ 47350699 47350699 0 GAGGGCAAA TTTGCTCTC 9 15.4 •••••••••• 5.5·10−9 588 PCBP4 Poly(rC)-binding protein 4 isoform a DA 3− 51993592 51992365 1227 GAGAGGGGG CCCTCTCTC 9 19.2 ◦••••••••••◦ 1.8·10−26 589 PCCA Propionyl-CoA carboxylase alpha chain, AA trans 13+ 100909848 101077886 168038 TGTCATGTT AACATGACA 9 15.1 • • • • • • • • • ◦ 1.2·10−9 590 PCDH17 Protocadherin-17 precursor AD exon 13+ 58240601 58240660 59 AATCTGAAG CTTCAGATT 9 14 •••••••••• ◦ 2.7·10−6 591 PCDH8 Protocadherin-8 isoform 1 precursor DD cis 13− 53420231 53420231 0 CCCGGCTCCCC GGGGAGCCGGG 11 30.1 ••◦••••••••◦ 1.6·10−5 592 PCF11 Pre-mRNA cleavage complex 2 protein Pcf11 DD cis 11+ 82878547 82878547 0 GATGCTGAAT GTTCAGCATT 10 16.8 •••••••••• ◦ 9.9·10−1 593 PCGF5 Polycomb group RING finger protein 5 AD exon 10+ 93031394 93031454 60 TGCCTCTTAT GTAAGAGGCA 10 19 •••••••••••• 5.9·10−22 594 PCSK5 Proprotein convertase subtilisin/kexin type 5 AD exon 9+ 78749024 78749128 104 TTGCTTGTG CACAGGCAA 9 15.5 • • • • • • • • • ◦ 9.2·10−11 595 PDE6C Cone cGMP-specific 3’,5’-cyclic DA 10+ 95380541 95386561 6020 TCTTTTCCA TGGAAAAGA 9 15 • • • • • • • • • ◦ 9.2·10−21 −9 596 PDHB N/A DD cis X 3− 58416569 58416569 0 GTGCCTATA TATGGGCAC 9 16.5 •••••••◦•• ◦ 5.2·10 −9 597 PDLIM7 PDZ and LIM domain protein 7 isoform 1 DA intron X 5− 176918404 176918147 257 GGCCCCTCCC GGGAGGGGCT 10 26.5 ••••••••• 1.0·10 Supplementary Table 1: (continued)

598 PFN2 -2 isoform b AA trans 3− 149684373 149684051 322 ACACTTTTC GAAAGGTGT 9 13.4 •••◦•••••• ◦ 8.8·10−9 599 PHF1 PHD finger protein 1 isoform b DD trans 6+ 4862852 4863167 315 GGGGCTGGGGGG TCCCCCAGCCCT 12 31 •••••••••• 4.6·10−11 600 PHF12 PHD finger protein 12 isoform 1 AA cis 17− 27277264 27277264 0 TGCACACAC GTGTGTGCA 9 18.4 •••••••••• 4.0·10−5 601 PHF12 PHD finger protein 12 isoform 1 AA trans 17− 27277264 27234012 43252 AAGGGGGGAGAGG CCTCTCTCCCCTT 13 28.8 • • ◦ • • • • • • • 2.0·10−11 602 PHF20L1 PHD finger protein 20-like protein 1 isoform 1 AD 8+ 133811340 133836305 24965 TTTCTGTTC GAACAGAAA 9 13.9 •••••••••••◦ 5.3·10−20 603 PHF20L1 PHD finger protein 20-like protein 1 isoform 1 DA 8+ 133823373 133837508 14135 GTAGCATTT AAATGCTGC 9 14 ••••••••◦•◦ 4.2·10−20 604 PHF20L1 PHD finger protein 20-like protein 1 isoform 1 AA cis 8+ 133826881 133826881 0 TTTTGGTTT AAGCCAAAA 9 12.1 ••••• •••••◦ 7.9·10−6 605 PHF21A PHD finger protein 21A isoform a DD trans 11− 46098304 45967626 130678 CATTGTGTT AATACAATG 9 11.7 ◦ • • • • • • • • • 2.5·10−5 606 PICALM Phosphatidylinositol-binding clathrin assembly AD 11− 85695016 85692914 2102 TTCCATTTT GAAATGGAA 9 12.9 • • ◦ • • • • • • • 1.3·10−17 607 PIGA Phosphatidylinositol DD trans X− 15349995 15349711 284 GGCGTGGAA TTCCACGCC 9 20 • • • • • • • ◦ • • 7.8·10−11 608 PLCE1 1-phosphatidylinositol-4,5-bisphosphate AA trans 10+ 95891930 96053264 161334 AATAAGTCA TGGCTTATT 9 12.4 ••••••••• 1.3·10−10 609 PLCG1 1-phosphatidylinositol-4,5-bisphosphate DD trans 20+ 39791365 39794191 2826 CCCTGCCCC GGGGCAGGG 9 24.1 ••••••••• 3.1·10−14 −16 610 PLEKHA1 Pleckstrin homology domain-containing family A AD exon X 10+ 124187791 124187936 145 GGTTAACTC GAGTTAACC 9 15.3 ••••••••◦• ◦ 1.1·10 611 PLSCR3 3 DD trans 17− 7297795 7297422 373 AAGGGAGGGG CCCCTCCCTT 10 24 ••••••••• 1.0·10−11 612 PLXNA1 Plexin-A1 precursor DD trans 3+ 126723851 126746929 23078 GGGGTGGGGG CCCCCACCCC 10 27.4 •••••••◦•• ◦ 7.3·10−26 613 POU4F2 POU domain, class 4, transcription factor 2 DA intron 4+ 147560580 147561018 438 AAGGCACAT GTGTGCCTT 9 17.5 •••••••••• 1.4·10−8 614 POU6F2 POU domain, class 6, transcription factor 2 AA cis 7+ 39125459 39125459 0 AGAGTGTGTGT ACACGCACTCT 11 21.3 •••••••••• 2.1·10−4 615 PPIP5K2 Inositol hexakisphosphate and DA intron 5+ 102515889 102518934 3045 AAAATACAG CTGTATTTT 9 11.5 ••••• •••••◦ 3.9·10−17 616 PPM1B Protein phosphatase 1B isoform 4 AA cis 2+ 44459454 44459454 0 AAAGGAAGG TCTTCCTTT 9 14.1 ••◦••••◦•••◦ 5.3·10−13 617 PPP1R12A Protein phosphatase 1 regulatory subunit 12A DA intron 12− 80199945 80199548 397 TGGATTTTTT AAAAAATCCA 10 13.4 ••••••••••• 2.8·10−14 618 PPP3CB Serine/threonine-protein phosphatase 2B DA 10− 75230644 75199659 30985 TGTACAGAA TTCTGTACA 9 15.3 ••••••••••• 4.5·10−9 −9

18 619 PPP3CB Serine/threonine-protein phosphatase 2B AA trans 10− 75230539 75198178 32361 CAAGATGCA TGCATTTTG 9 13.6 ◦•◦••••••• • 6.2·10 −11 620 PRG4 Proteoglycan 4 isoform B DD cis X 1+ 186274054 186274054 0 GCATTGATA TATCAATGC 9 14.4 •••••••••• 7.3·10 621 PRKCG gamma type DA 19+ 54387497 54396241 8744 GGGAGGGGG CCCTCTCCC 9 21.3 ••••••◦•••◦◦ 2.9·10−17 622 PRKCG Protein kinase C gamma type DD trans 19+ 54386448 54393271 6823 GGGGTGTGG CCACACTCC 9 18.8 ••••••••• 4.3·10−17 623 PRPF39 Pre-mRNA-processing factor 39 DD cis 14+ 45565431 45565431 0 TAGGTACTGT GCAGTACCTA 10 19.1 ••••••••••◦◦ 3.2·10−11 624 PRPF40B Pre-mRNA-processing factor 40 homolog B isoform AD 12+ 50026378 50028238 1860 CATGGCCTG CAGGCCATG 9 19.5 • • • • • • • • • ◦ 2.9·10−9 625 PRPF40B Pre-mRNA-processing factor 40 homolog B isoform AA trans 12+ 50026378 50037882 11504 CTCTTTCTT AAGAAGGAG 9 13.5 • • • • • • • ◦ • • 3.5·10−14 626 PRPF40B Pre-mRNA-processing factor 40 homolog B isoform AD 12+ 50026378 50031367 4989 GGGCTTGGC GCCAGGCCC 9 21.5 • • • • • • • • • ◦ 8.6·10−9 627 PRPF40B Pre-mRNA-processing factor 40 homolog B isoform DD trans 12+ 50024408 50031367 6959 GGGCTTGGC GCCAGGCCC 9 21.5 • • • • • • • • • ◦ 1.5·10−12 628 PRPF40B Pre-mRNA-processing factor 40 homolog B isoform DD trans 12+ 50026406 50031367 4961 GGGGGCCTG CAGGCTCCC 9 21.1 • • ◦ • • • • • • • 5.9·10−10 629 PSMD11 26S proteasome non-ATPase regulatory subunit 11 DA 17+ 30781637 30807770 26133 GTCAGTTTCT AGAAACTGAC 10 17.3 •••••••••• 1.0·10−16 630 PSMD11 26S proteasome non-ATPase regulatory subunit 11 DA 17+ 30781637 30791538 9901 GAAAGAAAT ATTTCTTTC 9 11.6 ••◦••••••• ◦ 4.2·10−22 631 PSMD12 26S proteasome non-ATPase regulatory subunit 12 DD trans 17− 65362527 65343451 19076 GCTGAGTCA TGATTCAGC 9 16.5 •••••••••• 1.9·10−19 632 PSMD14 26S proteasome non-ATPase regulatory subunit 14 AA trans 2+ 162175332 162241974 66642 TTTGTTTCTG CAGAAACAGA 10 14.6 ••••••••• 1.5·10−5 633 PTBP2 Polypyrimidine tract-binding protein 2 AA cis 1+ 97271974 97271974 0 ATCCATGAC GTTATGGAT 9 14.5 •••••••••••• 2.6·10−1 634 PTBP2 Polypyrimidine tract-binding protein 2 DD trans 1+ 97272008 97278484 6476 TCTTTTGCTA TAGCAGAAGA 10 16.2 ••••••••••◦◦ 1.2·10−15 635 PTPRD Receptor-type tyrosine-protein phosphatase delta DD trans 9− 8523512 8437197 86315 CTGCATTGT ACAGTGCAG 9 16 ••••••••◦• ◦ 2.7·10−7 636 PTPRD Receptor-type tyrosine-protein phosphatase delta AA trans 9− 8525035 8523524 1511 CAGGGCTTT AAAGCCTTG 9 15.4 •••••◦••◦• • 1.8·10−11 637 PTPRD Receptor-type tyrosine-protein phosphatase delta DA 9− 8523512 8499840 23672 GAATACAAA TTTGTATTC 9 11.8 ••••••••◦• • 2.4·10−11 −4 638 PTPRD Receptor-type tyrosine-protein phosphatase delta AD exon X 9− 8523524 8523512 12 TCATTTCATT AATGAAATGA 10 13.9 ••••••••••• 4.3·10 639 PTPRD Receptor-type tyrosine-protein phosphatase delta AD 9− 8526644 8523512 3132 TGCATTCAT ATGAATGTA 9 13.2 ••••••••••• 9.2·10−4 640 PTPRD Receptor-type tyrosine-protein phosphatase delta DA 9− 8527344 8521546 5798 ATGGCATGCA TGCATGTCAT 10 18 •••••••••◦ ◦ 2.1·10−14 641 PTPRN Receptor-type tyrosine-protein phosphatase-like DD trans 2− 220173939 220155259 18680 GGGGGAGGC GCCTCCTCC 9 21.4 •••••••••• 3.6·10−23 642 PTPRU Receptor-type tyrosine-protein phosphatase U AA trans 1+ 29581786 29585016 3230 AGGGAGGAGG CCTCCTCTCT 10 21.3 ••◦•••••••◦ 3.5·10−23 643 PTPRU Receptor-type tyrosine-protein phosphatase U AA trans 1+ 29581786 29652110 70324 AGAGGGAGGGA TCCCTCCCTCT 11 26.7 • • • • • • • • ◦ • 1.1·10−20 Supplementary Table 1: (continued)

644 PTPRU Receptor-type tyrosine-protein phosphatase U AD 1+ 29581786 29633658 51872 GGGAGGAGGG TCCTCCTCCT 10 22.5 •••••••••• 7.5·10−18 645 PUM2 Pumilio homolog 2 AA cis 2− 20478580 20478580 0 ATCACAGTAAT ATTATTGTGAT 11 15.2 •••••••••• 1.5·10−6 646 QKI Protein quaking isoform HQK-5 AA trans 6+ 163986977 163991725 4748 GAGATTGGT ACTAATCTC 9 14.2 ••••• ••••◦◦ 4.1·10−6 647 QKI Protein quaking isoform HQK-5 AA cis 6+ 163991725 163991725 0 GATTAGTTT AAACTAATC 9 11.8 •••••••••••• 1.9·10−2 648 R3HDM1 R3H domain-containing protein 1 AA trans 2+ 136373721 136393657 19936 ATCTTTCTT AAGAGAGAT 9 12.9 •••••◦••◦• • 1.6·10−19 649 R3HDM1 R3H domain-containing protein 1 DA 2+ 136393568 136437742 44174 TTGAAAGAT GTCTTTCAA 9 13.1 •◦•••••••• ◦ 2.0·10−25 650 RAB6A Ras-related protein Rab-6A isoform b AA cis 11− 73427407 73427407 0 GGCACATTA TAATGTGCC 9 16.4 •••◦ ••••••◦ 7.0·10−14 651 RALGAPA2 Ral GTPase-activating protein subunit alpha-2 DD trans 20− 20527347 20392670 134677 AACAGGTGT ACACCTGTT 9 17.1 ••••••••••• 6.8·10−15 652 RAPGEF4 Rap guanine nucleotide exchange factor 4 isoform DA 2+ 173855653 173901355 45702 TACAATAGCA TGCTATTGTG 10 16.2 ••••••••• 8.6·10−8 653 RAPGEF4 Rap guanine nucleotide exchange factor 4 isoform DD trans 2+ 173787028 173894982 107954 AAGGTAAAA TTTTGCCTT 9 12.5 • • • • • • • ◦ • • 1.9·10−15 654 RAPGEF4 Rap guanine nucleotide exchange factor 4 isoform DA 2+ 173855653 173885345 29692 CTAATCACAC GTGTGATTAG 10 16.4 •••••••••• 1.0·10−9 −13 655 RAPGEF6 Rap guanine nucleotide exchange factor 6 isoform DA intron X 5− 130785715 130782396 3319 ATTAATGCA TGCATTAAT 9 12.9 • • • • • • • • • ◦ 1.6·10 −5 656 RBBP6 E3 ubiquitin-protein ligase RBBP6 isoform 2 AA cis X 16+ 24579112 24579112 0 GGAAAACTAA TTAGTTTTCT 10 13.7 •••••••◦••◦◦ 6.4·10 657 RBFOX1 Fox-1 homolog A isoform 1 DA 16+ 7714970 7721558 6588 CAAGTTTGCT AGCAAACTTG 10 16.7 •••••••••• 2.1·10−17 658 RBFOX1 Fox-1 homolog A isoform 1 DA intron 16+ 7637302 7645550 8248 GGGGAAACAAC GTTGTTTTCCC 11 18.6 ••◦•• •••••◦ 4.9·10−15 659 RBFOX3 Fox-1 homolog C AA cis 17− 77092774 77092774 0 GGAGCAAACG CGTTTGCTTC 10 16.8 • • • • • • • • • ◦ 4.1·10−4 660 RBM10 RNA-binding protein 10 isoform 2 AD X+ 47035898 47045029 9131 GGGCTCGCT GGCGAGCCC 9 22.4 •••••◦••••◦ 1.0·10−16 661 RBM26 RNA-binding protein 26 AA trans 13− 79939853 79928696 11157 TGTATTACC GGTAATGCA 9 14.4 •••••••••◦ ◦ 5.8·10−20 662 RBM39 RNA-binding protein 39 isoform a AD 20− 34317287 34300940 16347 AGGAAAGATT AATCTTTTCT 10 13.2 ••◦•••••••◦ 3.6·10−15 663 RBM39 RNA-binding protein 39 isoform a DD cis 20− 34300940 34300940 0 GAATTGAAT ATTCAATTC 9 11.8 •••••◦••••◦◦ 1.0·10−15 −6 664 RBM5 N/A DD cis X 3+ 50138038 50138038 0 TGGAACAAG TTTGTTCCA 9 14.5 •••••••••• ◦ 2.3·10 −6

19 665 RBM5 N/A AA trans 3+ 50137964 50147811 9847 TTGTAAAGCT GGCTTTACAG 10 15.6 • • • • • • • • ◦ • 3.2·10 666 RBM5 N/A AD 3+ 50137964 50145580 7616 AAAGCTGCT AGCAGCTTT 9 17 •••••••◦•• ◦ 5.2·10−14 667 RBM5 N/A AA cis 3+ 50140515 50140515 0 TGTCCATTT AAATGGACA 9 15 •••••••••• ◦ 1.7·10−1 668 RCSD1 CapZ-interacting protein DA intron 1+ 167653238 167654657 1419 AGGGAGGAGG CTTCCTCCCT 10 21.6 •••••••••• ◦ 1.4·10−25 669 REPS1 RalBP1-associated Eps domain-containing protein DA 6− 139265634 139237113 28521 GTGACATTTT AAAATGTCAT 10 14 ••◦••••••• ◦ 1.0·10−19 670 RERE Arginine-glutamic acid dipeptide repeats protein DA 1− 8674619 8482867 191752 AAAATAGGA TCCTGTTTT 9 12.9 • • • • • • • • ◦ • 2.2·10−9 671 RERE Arginine-glutamic acid dipeptide repeats protein DD trans 1− 8674619 8482786 191833 TTAAAGGAG TTCCTTTAA 9 12.4 • • ◦ • • • • • • • 4.0·10−10 672 RERE Arginine-glutamic acid dipeptide repeats protein DA intron 1− 8674619 8617582 57037 AAGGAGAATC GATTTTCCTT 10 15 •••••••••• 5.5·10−11 673 RNF111 E3 ubiquitin-protein ligase Arkadia AA cis 15+ 59384735 59384735 0 TCAGTTGTT AACAACTGA 9 14.9 ••••••••••◦◦ 3.6·10−12 674 RNF111 E3 ubiquitin-protein ligase Arkadia AA trans 15+ 59376327 59384735 8408 AACCAATTA TGATTGGTT 9 12.8 •••••••◦••◦ 6.4·10−16 675 RNF41 E3 ubiquitin-protein ligase NRDP1 isoform 2 DD trans 12− 56615686 56615543 143 CCTCCTTCCC GGGGAGGAGG 10 22.6 • • • • • • • ◦ • • 4.8·10−18 676 ROBO1 Roundabout homolog 1 isoform d AA trans 3− 78717199 78685093 32106 CCTTCAGGT ATCTGAAGG 9 15.8 •••••••••• ◦ 3.2·10−13 677 RORA Nuclear receptor ROR-alpha isoform b AA trans 15− 60824050 60806956 17094 AGCAGGTTA TAACCTGTT 9 15 •••••••••◦◦ 3.0·10−11 678 RPGRIP1L Protein fantom isoform a DA 16− 53730062 53698921 31141 AAAAGCTTTTAG CTAAAAGCTTTT 12 16.4 ••••••••••◦ 1.1·10−12 679 RPS6KC1 Ribosomal protein S6 kinase delta-1 isoform a DA 1+ 213349835 213405465 55630 AACAAAAGG CTTTTTGTT 9 10.6 ••◦••••••• ◦ 1.9·10−7 680 RPS6KC1 Ribosomal protein S6 kinase delta-1 isoform a AA trans 1+ 213349742 213415911 66169 TCTTCCATT AATGGAAGA 9 15.2 ••••••••••• 2.9·10−6 681 RPS6KC1 Ribosomal protein S6 kinase delta-1 isoform a DD trans 1+ 213349835 213415640 65805 TGAAGCTTT AGAGCTTCA 9 14.9 •••••••••• ◦ 3.4·10−6 682 RUNX1T1 Protein CBFA2T1 isoform B AD 8− 93088365 92988132 100233 TTGTTGTTGT ACAACAACAA 10 15.6 •••••••••• ◦ 3.1·10−17 −19 683 RUSC2 Iporin DA intron X 9+ 35539105 35546426 7321 GAGAGGGGG CCCTCTCTC 9 19.2 •••••••••• 9.9·10 684 RXRB RXR-beta DA 6− 4620662 4619922 740 CAGGGTGCT AGTACCCTG 9 18.6 •••••••••◦ ◦ 1.2·10−17 685 SATB1 DNA-binding protein SATB1 isoform 1 AA trans 3− 18457625 18456726 899 TCAAACAGA TCTGTTTGA 9 15.1 • • • • • • • • • ◦ 2.5·10−12 686 SEMA3F Semaphorin-3F precursor AA cis 3+ 50222875 50222875 0 GGGGAAGGGG CCCCTTCCCC 10 25.2 ••••••••◦• ◦ 5.2·10−12 687 SEMA6A Semaphorin-6A precursor AD exon 5− 115832009 115831946 63 AAGCTTTCA TGAAGGCTT 9 14.5 ••••◦••••◦ • 1.1·10−16 688 SETD1B Histone-lysine N-methyltransferase SETD1B DD trans 12+ 122255424 122265760 10336 TCCTCGTCCT AGGACGAGGG 10 21.7 • • • • • • • • • ◦ 1.1·10−19 689 SEZ6L2 Seizure 6-like protein 2 isoform 3 DA 16− 29910261 29908232 2029 GGGGGTGGG CCCGCCCCC 9 23.7 •••••••••• 1.3·10−17 Supplementary Table 1: (continued)

690 SEZ6L2 Seizure 6-like protein 2 isoform 3 DA 16− 29910261 29884064 26197 GGGGGAGGGGA TCCCCTCCCCC 11 30 • • • • • • • • • ◦ 3.7·10−18 691 SF1 Splicing factor 1 isoform 5 DD trans 11− 64534371 64533422 949 GGGGGTGGGGC GCCCCGCCCCC 11 30.4 • • • • • • • • • ◦ 2.8·10−12 692 SF1 Splicing factor 1 isoform 5 AA trans 11− 64537880 64532990 4890 AGGCAGAGGG CCCTTTGCCT 10 21.5 • • • • • • • • ◦ • 2.7·10−9 693 SF1 Splicing factor 1 isoform 5 DA 11− 64540901 64535316 5585 CTGGTGGCAACAT ATGTTGCCACTAG 13 24.6 ••••••••••◦ 3.2·10−19 694 SF1 Splicing factor 1 isoform 5 DA 11− 64540901 64534551 6350 TTACCTTTTTC GGAAAAGGTAA 11 15.3 •••••••• •◦• 3.7·10−20 695 SF1 Splicing factor 1 isoform 5 AA cis 11− 64532990 64532990 0 GGGCGCCAG CTGGCGCCC 9 23.3 • • ◦ • • • • • • • 7.5·10−1 696 SF1 Splicing factor 1 isoform 5 DA intron 11− 64535577 64535316 261 TGGCAACATTGTTCTT AAGAACAATGTTGCCA 16 28.7 •••••••••• 1.1·10−17 697 SF1 Splicing factor 1 isoform 5 DD trans 11− 64540901 64533422 7479 TGGTGGCAA TTGTCACCA 9 16.7 •••••••••• ◦ 4.0·10−9 −13 698 SF1 Splicing factor 1 isoform 5 AD exon X 11− 64540977 64540901 76 TTTCCTAAC GTTGGGAAA 9 13.7 ••••••••••◦• 1.0·10 −14 699 SF1 Splicing factor 1 isoform 5 DA intron X 11− 64534371 64533627 744 GGGGGTGGGTGGG CCCACCCGCCCCC 13 34.6 • • • • • • • • • ◦ 8.0·10 700 SHANK1 SH3 and multiple ankyrin repeat domains protein DA 19− 51200352 51192225 8127 GGGATGGGG CCCCATCCC 9 22.1 ••••••••• 2.4·10−11 701 SHANK1 SH3 and multiple ankyrin repeat domains protein AD exon 19− 51200379 51200352 27 TCCCCTCCCT AGGGAGGGGA 10 25.5 •••••••••• 2.6·10−18 702 SHC1 SHC-transforming protein 1 isoform 1 DD trans 1− 154942507 154941853 654 CTCCTCTCC GGAGGGGAG 9 19.2 •••••••◦••◦ 1.5·10−27 703 SHC1 SHC-transforming protein 1 isoform 1 DA intron 1− 154946723 154942675 4048 CCTCTCCCC GGGGAGGGG 9 21.3 • • ◦ • • • • • • • 2.3·10−12 704 SHC1 SHC-transforming protein 1 isoform 1 AA trans 1− 154942675 154941310 1365 GGGGAGGGGA TCCCCTCCCC 10 26.7 •••••••••• 1.7·10−11 705 SIK3 Serine/threonine-protein kinase SIK3 DD cis 11− 116741046 116741046 0 TCCTTGGGCAG CTGCCCAAGGA 11 25 ◦•••••••••◦◦ 1.5·10−9 706 SKIV2L Helicase SKI2W DA 6+ 31928114 31937291 9177 TACAACCTC GAGGTTGTA 9 16.5 •••••••◦•• ◦ 1.5·10−22 707 SLC12A4 Solute carrier family 12 member 4 isoform b DD trans 16− 67991800 67979871 11929 CCATCTCCA TGGAGGTGG 9 18.2 •••••◦••••◦◦ 7.5·10−27 708 SLC12A5 Solute carrier family 12 member 5 isoform 1 DD trans 20+ 44663681 44664174 493 TCTCTCCCTCC GGAGGGAGGGA 11 24.9 •••••••••• 4.6·10−21 709 SLC12A5 Solute carrier family 12 member 5 isoform 1 AD exon 20+ 44664042 44664174 132 CCCTCCCTCCA TGGAGGGAGGG 11 27.6 •••••••••• ◦ 1.3·10−26 710 SLC12A5 Solute carrier family 12 member 5 isoform 1 DA 20+ 44664174 44669967 5793 GGGAGGGAA TTCTCTCCC 9 18 ••◦••••••• ◦ 2.4·10−25 −6

20 711 SLC20A1 Sodium-dependent phosphate transporter 1 DD cis 2+ 113410375 113410375 0 CTGGCCTGC GCAGGCTAG 9 19.5 •••••◦••••◦◦ 7.5·10 −4 712 SLC24A2 Sodium/potassium/calcium exchanger 2 isoform 2 AA cis X 9− 19597277 19597277 0 TTTGCACAT ATGTGTAAA 9 12.8 •••••••••• ◦ 2.8·10 713 SLC39A7 Zinc transporter SLC39A7 DA 6+ 4450022 4450828 806 GGCCCAGAG CTCTGGGCT 9 20.8 • • • • ◦ • • • • • 1.6·10−18 714 SLC6A16 Orphan sodium- and chloride-dependent DD trans 19− 49813609 49813296 313 TCCCTTTTCC GGAGAAGGGA 10 19.6 •••••••••• ◦ 9.2·10−25 715 SLC6A16 Orphan sodium- and chloride-dependent DD trans 19− 49813296 49812557 739 GGGAGAGGGA TCCCTCTCTC 10 21.6 •••••••••• 3.2·10−20 716 SLC6A6 Sodium- and chloride-dependent taurine DD cis 3+ 14509720 14509720 0 GGTGGTGGG CCCGCCACC 9 21.4 •••••••••••• 2.0·10−15 717 SLC6A9 Sodium- and chloride-dependent glycine AD 1− 44468088 44466627 1461 TCCTGGAGG CTTCCAGGA 9 18.3 • • • • • ◦ • • • • 1.1·10−17 −4 718 SLC8A1 Sodium/calcium exchanger 1 isoform B DD cis X 2− 40404891 40404891 0 GTGTGAGAGTA TACTCTCACAC 11 21.1 • • • • • • • • • ◦ 5.3·10 719 SLTM SAFB-like transcription modulator isoform a AA trans 15− 59192136 59192082 54 ACTTCTTGT ACAAGAAGT 9 14.9 ••••••••••• 7.9·10−6 720 SMARCA2 Probable global transcription activator SNF2L2 AD 9+ 2081831 2170472 88641 CAGATCTTG CAGGATCTG 9 14.9 • • • • • • • • • ◦ 2.5·10−18 721 SMARCC2 SWI/SNF complex subunit SMARCC2 isoform b DA 12− 56566720 56558152 8568 TAGGTGGGG CCCCACCTA 9 20.9 •••••••••• ◦ 1.0·10−10 −2 722 SMARCC2 SWI/SNF complex subunit SMARCC2 isoform b DA intron X 12− 56558431 56558152 279 GGGTTTGCC GGCGAACCC 9 19.1 •••••••••• ◦ 4.6·10 723 SMARCC2 SWI/SNF complex subunit SMARCC2 isoform b DD trans 12− 56563559 56558431 5128 GGGCAGGAG CTCCTGCTC 9 19 • • • • • • • • • ◦ 8.8·10−14 724 SMARCD1 SWI/SNF-related matrix-associated DA 12+ 50480131 50483666 3535 GGGAGGGAGG CTTCCCTCCC 10 22.8 •••••••••• ◦ 3.9·10−21 725 SMARCE1 SWI/SNF-related matrix-associated DD trans 17− 38802047 38798706 3341 TCAGTTGTTT AAACAACTGG 10 14.9 •••••••◦••◦◦ 5.4·10−15 726 SMARCE1 SWI/SNF-related matrix-associated AD 17− 38802099 38798706 3393 TTGATTCTCTT AGGAGAATCAA 11 17 • • • • ◦ • • • • • 1.1·10−13 727 SMEK2 Serine/threonine-protein phosphatase 4 DA 2− 55808702 55791633 17069 GTAAGAAAT ATTTCTTAC 9 11.8 ••◦••••••• ◦ 2.5·10−24 728 SMG6 Telomerase-binding protein EST1A isoform 2 DD trans 17− 2147951 2075951 72000 TATTTTCCT GGGAAAATA 9 12.9 • • ◦ • • • • • • • 2.4·10−4 729 SMG6 Telomerase-binding protein EST1A isoform 2 AA cis 17− 2148013 2148013 0 TCCCTAGTG CACTGGGGA 9 18.5 •••••••••• ◦ 3.0·10−2 730 SMG7 Protein SMG7 isoform 2 AD 1+ 183486822 183511499 24677 CTTTCTTGTT AACAGGAAAG 10 14.2 • • • • • • • • • ◦ 3.2·10−8 −13 731 SMTN Smoothelin isoform c AD exon X 22+ 31496870 31496939 69 TGTATGTGT ACACGTACA 9 14.9 ••••••••••◦ 1.3·10 732 SMTN Smoothelin isoform c DA 22+ 31484592 31496870 12278 GGGGCAGGG TCCTGCCCC 9 22.3 ••◦•••••••◦ 2.7·10−18 733 SMTN Smoothelin isoform c DA 22+ 31479295 31496870 17575 GAGAGGCAGGG CTCTGCCTCTT 11 22.4 ••••••••• 4.5·10−13 734 SMYD1 SET and MYND domain-containing protein 1 DD cis 2+ 88393074 88393074 0 GTGGGTCAG CTGACCCAT 9 18.9 • • • • • • • • • ◦ 1.8·10−13 735 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa AA trans 2− 96944449 96940893 3556 CTGCAGGGTC GACCTTGCAG 10 20.3 • • • • • • • • ◦ • 1.1·10−18 Supplementary Table 1: (continued)

736 SORBS1 Sorbin and SH3 domain-containing protein 1 AA trans 10− 97174412 97081778 92634 GATTTCATT AATGAGATC 9 11.9 •••••••••• 1.4·10−10 737 SORBS2 Sorbin and SH3 domain-containing protein 2 DD trans 4− 186877349 186731901 145448 TTTGTTCCT AGGAACAAA 9 14.8 ••••••••• 1.1·10−16 738 SORBS2 Sorbin and SH3 domain-containing protein 2 AA trans 4− 186696520 186508842 187678 CTGAAAATAG CTATTTTCAG 10 13.8 •••••••••◦ ◦ 4.5·10−22 739 SOX2OT N/A DD cis 3+ 181328717 181328717 0 TAATTGACTTG CAAGTCAATTG 11 15.7 ••••••••••◦◦ 2.5·10−8 740 SOX6 Transcription factor SOX-6 isoform 3 AD 11− 16133469 16119154 14315 TGTTTAGCA TGCTAAATA 9 13.1 ••◦••••••• ◦ 3.2·10−15 741 SPEG Striated muscle preferentially expressed protein AD 2+ 220312695 220356591 43896 GGGGTGGGGG CCCCTACCCC 10 25.1 •◦•••••••• ◦ 1.2·10−23 742 SPI1 Transcription factor PU.1 isoform 1 DD cis 11− 47381403 47381403 0 CAGGAAGCT AGCTTCCTG 9 18.4 •••••••◦•• ◦ 5.3·10−15 743 SPTBN5 Spectrin beta chain, brain 4 AA trans 15− 42162758 42154121 8637 AGCGGGAGG CCTCCCGCT 9 22.3 • • • • • • • • • ◦ 1.2·10−23 744 SR140 U2-associated protein SR140 AD 3+ 142745990 142747248 1258 ATCCATTTT AAAATGGAT 9 12.7 • • • • • • • • • ◦ 2.7·10−12 745 SR140 U2-associated protein SR140 AD 3+ 142747324 142757802 10478 AGGTTCTTA TAAGAATCT 9 12.6 • • • • • • • • • ◦ 1.4·10−14 746 SRCAP Helicase SRCAP DA 16+ 30723065 30732033 8968 GAAGATGAA TTCATTTTC 9 11.7 •••••••••• 9.2·10−20 747 SRCAP Helicase SRCAP DD trans 16+ 30723065 30733607 10542 GGAGGAAGAA TTTTTCCTCC 10 17.2 • • • • • ◦ • • • • 2.8·10−17 748 SREK1 Splicing factor, arginine/serine-rich 12 isoform AA trans 5+ 65455046 65460610 5564 ATAGTGTAA TTGCACTAT 9 13.2 ••••• ••••◦◦ 1.9·10−11 749 SREK1 Splicing factor, arginine/serine-rich 12 isoform AD 5+ 65454636 65458420 3784 CTTCTTTTC GAAAGGAAG 9 12.3 ••••• ••••◦◦ 1.3·10−11 750 SRSF1 N/A AA cis 17− 56081362 56081362 0 TTTTGGGGAAT ATTCCCCAGAA 11 19.2 •••••••••••◦ 8.9·10−1 751 SRSF10 N/A DA 1− 47744 41459 6285 TAGTGACAA TTGTCACTG 9 15 ••••◦••••• ◦ 1.4·10−14 −2 752 SRSF3 N/A AD exon X 6+ 36567597 36568053 456 TTTGGTCCA TGGATCAAA 9 14.6 • • • • • • • • • ◦ 6.6·10 −1 753 SRSF3 N/A AA cis X 6+ 36567597 36567597 0 TGAAAAACAA TTGTTTTTCA 10 13.3 ••••••••••• 9.0·10 −1 754 SRSF6 Serine/arginine-rich splicing factor 6 DD cis X 20+ 42088060 42088060 0 GTTAAGTTT AAACTTAGC 9 11.4 •••••••••••• 9.9·10 755 SRSF7 Serine/arginine-rich splicing factor 7 isoform DD trans 2− 38973835 38973285 550 TCCAAAGAGTTCAAAG CTTTGAGCTCTTTGGA 16 27.7 •••••••••••◦ 2.3·10−21 756 SSBP2 Single-stranded DNA-binding protein 2 AA trans 5− 80809536 80762860 46676 TGTAATGAT ATCATTACA 9 13.2 • • • • • • • • • ◦ 1.4·10−15 −15

21 757 SSBP3 Single-stranded DNA-binding protein 3 isoform c DD trans 1− 54867533 54704801 162732 GTAACAAAT ATTTGTTAC 9 11.6 ◦••••••••• • 1.2·10 758 SSBP3 Single-stranded DNA-binding protein 3 isoform c AA trans 1− 54723822 54722859 963 CTTTTAAGC GCTTAAAGG 9 12.2 ◦••••••••• ◦ 1.0·10−16 759 SSPO SCO-spondin precursor DD trans 7+ 149480110 149518638 38528 GGTGCAGGG TCCTGCACC 9 20 •••••••◦•• ◦ 1.1·10−26 760 STAG2 Cohesin subunit SA-2 isoform b DA X+ 123094716 123185164 90448 AGTTTGGAG TTCCAAACT 9 14.5 ••••••••• 1.7·10−10 761 STAG2 Cohesin subunit SA-2 isoform b DD trans X+ 123200112 123224614 24502 CTATGTAAT ATTACATAG 9 12.1 •••••◦•••• ◦ 1.9·10−13 762 STRN Striatin DD cis 2− 37113858 37113858 0 GGAAAACATTG CAATGTTTTCC 11 16.8 ••••••••••• 5.4·10−5 763 STRN3 Striatin-3 isoform 2 AD 14− 31398517 31382729 15788 AGACTGCAC GTGCAGTTT 9 16 ••••• •••••◦ 3.0·10−10 764 STXBP1 Syntaxin-binding protein 1 isoform b AD 9+ 130413881 130438221 24340 TCTCTTTCTC GAGAAAGAGG 10 16.8 ••••••••••◦ 1.2·10−30 765 SUFU Suppressor of fused homolog isoform 2 DD trans 10+ 104264091 104377185 113094 GGAGGAGGGG CCCCTCCTCT 10 24.3 •••••••••• ◦ 3.1·10−22 766 SYN1 Synapsin-1 isoform Ia DA X− 47434086 47432398 1688 TCCAGGCCC GGGCCTGGG 9 22.3 ••◦•••••••◦◦ 4.1·10−21 767 SYNGAP1 Ras GTPase-activating protein SynGAP DA intron 6+ 33406696 33408505 1809 GAGACTGGGA TCCCGGTCTC 10 21.6 •••••••••• 6.8·10−13 768 SYNGAP1 Ras GTPase-activating protein SynGAP DD trans 6+ 33403390 33410271 6881 GGAGGAGAG CTCTCCTCT 9 18.9 ••••••••• 2.1·10−16 769 SYNGAP1 Ras GTPase-activating protein SynGAP DD trans 6+ 33410271 33414563 4292 TCCCCTCCCC GGGGAGGGGG 10 25.8 ••••••••••• 1.4·10−21 770 SYNGAP1 Ras GTPase-activating protein SynGAP DA 6+ 33391375 33408505 17130 GAGAGAGACA TGTCTCTCTC 10 20.2 •••••••••• 5.9·10−14 −10 771 SYNJ1 Synaptojanin-1 isoform c DD cis X 21− 34007170 34007170 0 TAGATGTATG CATACATCTA 10 15.7 •••••••••••◦ 1.9·10 772 SYT7 Synaptotagmin-7 AD exon 11− 61300596 61300460 136 CCCAGCCCA TGGGCTGGG 9 22.9 •••••••◦•• ◦ 1.0·10−27 773 TADA3 Transcriptional adapter 3 isoform b DD trans 3− 9831396 9828882 2514 CTGGGCTTC GAGGCCCAG 9 19.3 • • • • • • • • • ◦ 1.4·10−17 774 TAF1 Transcription initiation factor TFIID subunit 1 AD X+ 70596862 70674707 77845 GAGAAGGCA TGTCTTCTC 9 16 ••••••••• 4.5·10−10 775 TAF15 TATA-binding protein-associated factor 2N AD exon 17+ 34160910 34160945 35 GCTCAGCAC GTGCTGAGT 9 18.9 •••••••◦••◦◦ 5.0·10−14 776 TAF4B Transcription initiation factor TFIID subunit DA 18+ 23901164 23915138 13974 TTAAAGGAA TTCCTTTGA 9 12.8 ••◦••••••• ◦ 4.9·10−21 777 TAOK2 Serine/threonine-protein kinase TAO2 isoform 1 AA trans 16+ 29989058 30000913 11855 GGGGAGGAGA TCTCCTCTCC 10 21.6 •••••••◦•• ◦ 9.7·10−21 778 TAOK2 Serine/threonine-protein kinase TAO2 isoform 1 AA trans 16+ 30000913 30002367 1454 CTCTGCTTC GGAGCAGAG 9 17 • • • • ◦ • • • • • 4.2·10−18 779 TAOK2 Serine/threonine-protein kinase TAO2 isoform 1 DD trans 16+ 29997825 30001126 3301 CCCGGGCCT AGGCCTGGG 9 22.2 ••◦••••••• ◦ 1.3·10−23 780 TAOK2 Serine/threonine-protein kinase TAO2 isoform 1 DA 16+ 29996899 30000913 4014 GGGAGAAGG TCTTCTCCC 9 18 • • ◦ • • • • • • • 8.8·10−17 781 TAOK2 Serine/threonine-protein kinase TAO2 isoform 1 DA intron 16+ 29997825 30000913 3088 GAGGAGGAGGAA TTCCTCCTCTTC 12 24 •••••••••• ◦ 4.8·10−17 Supplementary Table 1: (continued)

782 TAOK3 Serine/threonine-protein kinase TAO3 AD exon 12− 118627746 118627611 135 GAGAGAGAG TTCTCTCTC 9 16.5 ••◦••••••• ◦ 1.4·10−7 783 TASP1 Threonine aspartase 1 precursor AA cis 20− 13398168 13398168 0 ATGGAAAGT ATTTTCCAT 9 12.7 ••••••••• 3.7·10−3 784 TBX5 T-box transcription factor TBX5 isoform 3 DD trans 12− 114839630 114836377 3253 GGAGAGAGA TTTCTCTCC 9 16.6 • • ◦ • • • • • • • 1.9·10−27 785 TCF4 Transcription factor 4 isoform a AA cis 18− 52928764 52928764 0 TTAATGCTAATTA TAATTAGCATTAA 13 17.3 ••••••••••◦◦ 3.4·10−5 786 TCF4 Transcription factor 4 isoform a AD 18− 53070749 52899751 170998 CTGTTACCTG TAGGTAACAG 10 17.2 •••••••••••• 9.9·10−14 −5 787 TCF4 Transcription factor 4 isoform a DD cis X 18− 52899751 52899751 0 TCGCTTCAT ATGAAGTGA 9 14.9 •••••••••••• 1.5·10 788 TCF7L2 Transcription factor 7-like 2 isoform 7 AA trans 10+ 114905769 114921337 15568 AGAATAAAG CTTTGTTCT 9 11.7 • • • • • • • • • ◦ 4.3·10−11 789 TCF7L2 Transcription factor 7-like 2 isoform 7 AD 10+ 114724314 114920450 196136 GCTTTGATTT AAATCAAAGC 10 14.7 •••••••••• 2.7·10−9 790 TEAD1 Transcriptional enhancer factor TEF-1 AA trans 11+ 12883796 12886384 2588 CTTTCTTTC GAAAGAAAG 9 12.6 ••••••••◦•◦• 6.1·10−18 791 TERF1 Telomeric repeat-binding factor 1 isoform 1 DA 8+ 73926225 73942570 16345 GGGAAGAAA TTTCTTTCC 9 13.3 • • ◦ • • • • • • • 6.4·10−22 792 THOC1 THO complex subunit 1 AA cis 18− 224994 224994 0 CTACTATCT AGATGGTAG 9 14.3 ••◦•••••••◦ 4.2·10−11 793 THOC2 THO complex subunit 2 DA intron X− 122754757 122753287 1470 TAGAAAATGAA TTCATTTTCTA 11 15 •••••••••• ◦ 9.9·10−8 794 TLE1 Transducin-like enhancer protein 1 AA trans 9− 84300635 84268951 31684 AAAGACAGA TTTGTCTTT 9 12.5 •••••••••• 1.6·10−17 795 TLE1 Transducin-like enhancer protein 1 DA 9− 84268888 84228436 40452 TTTATCACAA TTGTGATAAA 10 13.9 ••◦••••••• ◦ 5.2·10−6 796 TLE1 Transducin-like enhancer protein 1 AA trans 9− 84228436 84202743 25693 GCTGTTGTG CACAACAGT 9 16.2 •••••••••◦ ◦ 1.3·10−11 797 TLE1 Transducin-like enhancer protein 1 AA trans 9− 84300635 84248279 52356 GACAGAAATG TATTTCTGTT 10 14 •••••••••• 1.5·10−8 798 TLE1 Transducin-like enhancer protein 1 AA trans 9− 84300811 84268951 31860 AAGGACAAAG CTTTGTCTTT 10 14.2 •••••••••• ◦ 4.2·10−18 799 TLE1 Transducin-like enhancer protein 1 DA 9− 84249011 84202743 46268 CAAGCCAGA TCTGGTTTG 9 16 •••◦•••••• ◦ 4.8·10−17 800 TLE1 Transducin-like enhancer protein 1 AD 9− 84300811 84268888 31923 GCAGATGTT AACATCTGT 9 15.4 •••••••◦•• ◦ 1.0·10−7 801 TLE3 Transducin-like enhancer protein 3 isoform b DD trans 15− 70387916 70366871 21045 GTGAGAGGC GCCTCTTAC 9 17.8 ◦ • • • • • • • • • 7.8·10−18 802 TLE4 Transducin-like enhancer protein 4 AA cis 9+ 82334960 82334960 0 TAGCATTAAT GTTAATGCTG 10 14.2 •••••••••• ◦ 2.7·10−4 −18

22 803 TLN2 -2 AD 15+ 63084839 63128272 43433 ATTTTCCTA TGGGAAAAT 9 12.6 ••••••••••◦ 1.2·10 804 TLN2 Talin-2 AD 15+ 62989886 63128272 138386 CAGTGACCA TGGTCACTG 9 18.5 • • • • • • • • • ◦ 9.2·10−20 805 TM9SF4 Transmembrane 9 superfamily member 4 precursor DA 20+ 30729468 30738602 9134 CCCGGCTGGA TCCAGCCGGG 10 25.6 •••••••◦•• ◦ 1.8·10−19 −7 806 TMPO Thymopoietin isoform alpha AA cis X 12+ 98926600 98926600 0 AGAGGCAAAG TTTTGCCTCT 10 17.8 •••••••••• 1.7·10 807 TNIK TRAF2 and NCK-interacting protein kinase isoform DA 3− 170879058 170824995 54063 AAGAATCCA TGGATTCTT 9 15.2 ••◦•••••◦•• 1.0·10−20 808 TNIK TRAF2 and NCK-interacting protein kinase isoform AD 3− 170893119 170783975 109144 TGGTCTCTT AAGAGACCA 9 17.5 ••◦••••••• ◦ 4.7·10−17 809 TNPO1 Transportin-1 isoform 2 DA intron 5+ 72192978 72195832 2854 AGAAACCAA TTGGTTTCT 9 14.8 ••••• ••••◦◦ 2.4·10−14 810 TNPO1 Transportin-1 isoform 2 AD exon 5+ 72195832 72195908 76 TGGTTGGCG TGCCAACCA 9 18.7 ••••••••••• 6.1·10−1 811 TNPO2 Transportin-2 isoform 1 DA 19− 12826218 12816212 10006 TCATCATGG CCATGGTGA 9 16 • • • • • • • • • ◦ 2.4·10−21 812 TOP2B DNA topoisomerase 2-beta DD trans 3− 25660144 25659908 236 AATAGAAGAC GTCTTCTGTT 10 15.4 • • ◦ • • • • • • • 2.7·10−9 813 TRIM3 Tripartite motif-containing protein 3 DA 11− 6479294 6472668 6626 GGTAGGGGG CCTCCTACC 9 19.1 • • • ◦ • • • • • • 3.0·10−15 −6 814 TRIM33 E3 ubiquitin-protein ligase TRIM33 isoform beta AA cis X 1− 114940612 114940612 0 TAGAAAGGAT ATCCTTTTTA 10 13.9 ••◦•• •••••• 9.7·10 815 TRIM55 Tripartite motif-containing protein 55 isoform DA 8+ 67062474 67067857 5383 GAGAAAATA TGTTTTCTC 9 12 ••◦•••••••◦◦ 2.1·10−23 816 TRPM1 Transient receptor potential cation channel DD cis 15− 31323185 31323185 0 TCCAAATTAA TTAATTTGGA 10 13.8 ••••••••◦•◦• 1.6·10−12 817 TTC7B Tetratricopeptide repeat protein 7B AD 14− 91247250 91196418 50832 TTTCTTTCT AGAAGGAAA 9 12.3 ••••◦••••••◦ 4.4·10−29 818 TTN isoform N2-A AD 2− 179622643 179476783 145860 TTCTTTTCA TGAGAAGAA 9 12.7 • • • • • • • • • ◦ 1.2·10−17 819 TTN Titin isoform N2-A DD trans 2− 179483310 179472511 10799 TGACAGAAACA TGTTTCTGTCA 11 19.4 •••••••••• ◦ 2.2·10−20 820 TTN Titin isoform N2-A DA 2− 179577041 179482808 94233 ACCGTATTT AAATATGGT 9 12.5 • • • • • • • ◦ • • 2.6·10−18 821 TTN Titin isoform N2-A DD trans 2− 179599433 179404794 194639 TCTTTCATC GATGAAAGA 9 14.3 ••◦••••••• ◦ 1.5·10−21 822 TTN Titin isoform N2-A AD 2− 179544143 179485441 58702 CAATATCTT AAGATATTG 9 11.9 ••••••••◦• ◦ 1.3·10−21 823 TTN Titin isoform N2-A DA 2− 179482915 179464172 18743 CTCCTTTGA TCAAAGGAG 9 16.2 ••••◦••••• ◦ 4.3·10−21 824 TTN Titin isoform N2-A AD 2− 179616766 179577041 39725 AATATGGTG CACCGTATT 9 13.7 • • • • • • • • • ◦ 4.0·10−18 825 TTN Titin isoform N2-A AA trans 2− 179582948 179457387 125561 GTCTGTCTT AAGACAGGC 9 15.8 ••◦••••••• ◦ 2.6·10−24 826 TTN Titin isoform N2-A DD trans 2− 179592311 179483310 109001 TGTTTCTGT ACAGAAACA 9 14.9 •••••◦•◦•• • 5.9·10−23 827 TTN Titin isoform N2-A DD trans 2− 179647265 179617850 29415 AAGAGATGT ATATCTCTT 9 13.4 • • • • • • • • ◦ • 4.5·10−17 Supplementary Table 1: (continued)

828 TTN Titin isoform N2-A DA 2− 179486201 179411229 74972 ATTTATCTC GAGATGAAT 9 12.3 •••••••◦•• ◦ 3.2·10−21 829 TTN Titin isoform N2-A AA trans 2− 179569504 179458202 111302 CATTTATTC GAATAAGTG 9 10.7 • ◦ • • • • • • • • 2.4·10−14 830 TTN Titin isoform N2-A AD 2− 179622643 179517184 105459 TTCTTTTCAG CTGAAAAGAA 10 14.7 •••••••••• ◦ 2.6·10−24 831 TTN Titin isoform N2-A AD 2− 179470022 179444665 25357 CAAGATGATG CATCATTTTG 10 13.7 •••••••••• ◦ 8.4·10−24 832 TTN Titin isoform N2-A AD 2− 179540722 179485828 54894 TGTCTTTAA TTAAGGACA 9 12.5 •••••••••• ◦ 1.9·10−25 833 TTN Titin isoform N2-A AA trans 2− 179622643 179523815 98828 TTCTTTTCAG CTGAAAAGAA 10 14.7 •••◦•••••• ◦ 1.1·10−24 834 TTN Titin isoform N2-A AA trans 2− 179587273 179466641 120632 CAAGGTGAT ATCATCTTG 9 13.6 ••••••◦••• ◦ 2.5·10−20 835 TTN Titin isoform N2-A AD 2− 179632651 179599433 33218 GATGAAAGA TCTTTCATC 9 14.3 • • ◦ • • • • • • • 1.2·10−19 836 TTN Titin isoform N2-A AD 2− 179482808 179479573 3235 AGCAAGGAGT GCTCCTTGCT 10 20.9 •••••••••• 3.6·10−19 837 TTN Titin isoform N2-A AD 2− 179622643 179486566 136077 GCTTCTTTT AGAAGAAGC 9 13.7 ••••••••◦• ◦ 1.1·10−21 838 TTN Titin isoform N2-A DD trans 2− 179483310 179470140 13170 CGTAACTTA TAAGTTGCG 9 13.3 •••••••••• ◦ 2.3·10−21 839 TTN Titin isoform N2-A AA trans 2− 179539840 179449305 90535 AAATGTCAA TTGGCATTT 9 12 ••◦••••••• ◦ 3.9·10−22 840 UBAP2L Ubiquitin-associated protein 2-like isoform a DD cis 1+ 154214041 154214041 0 TTCTATCCCT AGGGATAGAA 10 18.9 •••••••◦•• ◦ 1.8·10−8 841 UBE2E3 Ubiquitin-conjugating E2 E3 AA cis 2+ 181848769 181848769 0 ACAAAGAGG CCTTTTTGT 9 13.4 ••••••••◦• ◦ 3.0·10−3 842 UBR4 E3 ubiquitin-protein ligase UBR4 DD trans 1− 19467840 19467281 559 GGCAGTTAC GTAACTGTC 9 14.8 • • • • • ◦ • • • • 5.4·10−14 843 UBR4 E3 ubiquitin-protein ligase UBR4 DA 1− 19499674 19468018 31656 ACCACCATCT AGATGGTGGT 10 20.8 ••◦••••••• ◦ 9.2·10−21 844 UBR4 E3 ubiquitin-protein ligase UBR4 DA intron 1− 19467840 19467386 454 ACAGGTGGAGA TCTCCACTTGT 11 21.5 •••••◦•••• ◦ 7.3·10−20 845 UBR5 E3 ubiquitin-protein ligase UBR5 AD 8− 103306072 103291263 14809 CCAAAAAGA TCTTTTTGG 9 13.5 •••••••◦•• ◦ 3.2·10−21 846 UBR5 E3 ubiquitin-protein ligase UBR5 AA trans 8− 103354912 103306072 48840 CTTACTTTT AAAAGTAAG 9 11.3 • • • • • • • • • ◦ 6.4·10−14 847 UBTF Nucleolar transcription factor 1 isoform a DA 17− 42293021 42289822 3199 GGAGGGGAG TTCCCCTCC 9 20.7 • • • • • • • • • ◦ 9.0·10−20 848 UNC80 Protein unc-80 homolog isoform 2 DA 2+ 210694103 210849579 155476 GAGGAAAAG CTTTTCCTT 9 13.9 •••◦•••••• ◦ 1.1·10−19 −11

23 849 UPF2 Regulator of nonsense transcripts 2 DD trans 10− 12084912 12084753 159 GGAGGGGAGGG CCTTCCCCTCC 11 26.1 ••••••••••◦ 2.0·10 850 USH2A Usherin isoform B DD trans 1− 216221875 216051099 170776 GTAATTTCA TGAGATTAC 9 11.9 ••◦••••••• • 3.6·10−8 851 USP19 Ubiquitin carboxyl-terminal 19 AD 3− 49153371 49149921 3450 GCGCTGGGG CCCTAGCGC 9 21 •••••••••• ◦ 1.6·10−16 852 USP34 Ubiquitin carboxyl-terminal hydrolase 34 DA 2− 61484338 61417549 66789 ACAATGTTG CAACATTGT 9 13.6 ••◦••••••• ◦ 1.9·10−20 853 USP34 Ubiquitin carboxyl-terminal hydrolase 34 AA trans 2− 61431515 61430398 1117 TTGTACTTA TAAGTGCAA 9 13 ••••••••◦• ◦ 1.5·10−14 854 USP5 Ubiquitin carboxyl-terminal hydrolase 5 isoform DA 12+ 6965614 6970116 4502 GGGTAGGGAG CTCCCTACCC 10 23.3 ••◦••••••• ◦ 3.1·10−25 855 USP54 Inactive ubiquitin carboxyl-terminal hydrolase DA 10− 75294357 75258946 35411 AAAAGAAAC GTTTCTTTT 9 11.2 ••••••••• 4.2·10−19 856 VAMP2 Vesicle-associated membrane protein 2 DD cis 17− 8064925 8064925 0 GATGATGAT ATCATCATC 9 14.7 •••••◦••••◦◦ 6.5·10−19 857 VAMP4 Vesicle-associated membrane protein 4 isoform 1 DD cis 1− 171673526 171673526 0 TCAAATTGGA TCTAATTTGA 10 13.8 • ◦ • • • • • • • • 2.4·10−7 858 VARS Valyl-tRNA synthetase DD trans 6− 3065056 3062134 2922 GGGTGGGGG CCCTCACCC 9 21.1 ••••••••• 1.2·10−14 859 VEGFA Vascular endothelial growth factor A isoform k AD 6+ 43748468 43749789 1321 CTCTCTCTCT GGAGAGAGAG 10 20.1 ••••••••◦• ◦ 7.1·10−22 −15 860 VEGFA Vascular endothelial growth factor A isoform k AD exon X 6+ 43749692 43749789 97 CTCTCTCTG CAGAGAGGG 9 16.8 • • • • • • • • • ◦ 1.9·10 861 VPS16 Vacuolar protein sorting-associated protein 16 DA 20+ 2840797 2846044 5247 CTGCTCTGT GCAGAGCAG 9 18.8 • • • • • • • • • ◦ 3.1·10−15 862 VTI1A Vesicle transport through interaction with DD cis 10+ 114298089 114298089 0 AATTGTCTT GAGACAATT 9 13 ••••••••••• 6.8·10−1 863 VWA5B1 Von Willebrand factor A domain-containing DA 1+ 20644168 20657361 13193 GGGAAGGAA TTCCTTCTC 9 15.6 •••••••••• 2.5·10−21 864 WASF2 Wiskott-Aldrich syndrome member DA 1− 27755270 27744923 10347 TCCCTCTCC GGGGAGGGA 9 20.4 ••••••••••◦◦ 6.7·10−18 865 WIBG Partner of Y14 and mago isoform 2 DD trans 12− 56320859 56297170 23689 CCCCTCCTTT GAAGGAGGGG 10 22 • • • • • • • ◦ • • 5.4·10−15 −1 866 WNK3 Serine/threonine-protein kinase WNK3 isoform 1 DD cis X X− 54265441 54265441 0 AAAAAGCTGG CCAGCTTTTT 10 16.6 ••••••••• 9.6·10 867 WNT5A Protein Wnt-5a precursor AA trans 3− 55514946 55513592 1354 CGGATGCTT AAGCATCTG 9 15.5 • • ◦ • • • • • • • 6.4·10−7 868 WSB1 WD repeat and SOCS box-containing protein 1 DA intron 17+ 25633908 25636125 2217 TGCTCGGTGTC GACACTGAGCA 11 22.4 • • • • • • • • • ◦ 1.9·10−12 869 YTHDC1 YTH domain-containing protein 1 isoform 2 DA intron 4− 69188466 69185923 2543 TAGGCACAT ATGTGTCTA 9 14.9 ••••• ••••◦◦ 5.4·10−13 870 YTHDC1 YTH domain-containing protein 1 isoform 2 DD trans 4− 69203289 69188466 14823 CTTTTTCTT AAGAAAGAG 9 11.2 ••••••••• 6.2·10−8 871 ZBTB20 Zinc finger and BTB domain-containing protein 20 AA cis 3− 114099251 114099251 0 AAACAAGGG CCTTTGTTT 9 13 •••••••••• ◦ 9.9·10−1 872 ZBTB22 Zinc finger and BTB domain-containing protein DD cis 6− 4729469 4729469 0 CTTTAAAGG CCTTTAAAG 9 12.4 ••••••••◦•• 1.0·10−10 873 ZBTB38 Zinc finger and BTB domain-containing protein DD trans 3+ 141087646 141105779 18133 GCCATCTTG TAAGATGGC 9 16.3 •••••••••• 4.6·10−15 Supplementary Table 1: (continued)

874 ZEB2 N/A DD trans 2− 145161482 145153978 7504 ATTTCTTTCT AGGAAGAAAT 10 13.2 •••••••••◦ • 3.8·10−7 875 ZEB2 N/A DD trans 2− 145162402 145161482 920 AGCTGTTAC GTAATAGCT 9 14.4 ••◦•••••••◦◦ 1.5·10−7 876 ZEB2 N/A DD cis 2− 145162402 145162402 0 CCTCTGCAGCTGTT AACAGCTGCAGAGG 14 30.3 ••••••••••◦• 2.5·10−6 −13 877 ZFX Zinc finger X-chromosomal protein isoform 3 AD exon X X+ 24227016 24227216 200 GTCATTCATGAGTATCA TGATATTCATGAATGAT 17 26.9 •••••••••• 6.7·10 878 ZMYM3 Zinc finger MYM-type protein 3 isoform 1 DD trans X− 70473878 70466444 7434 GGTGGGGGGGT ACCCCTCCACC 11 26.6 ••••◦••••• ◦ 7.8·10−20 879 ZMYND8 Protein kinase C-binding protein 1 isoform a AD 20− 45927616 45918930 8686 GCCACTCAC GTGAGTGGC 9 19.8 ••••••••◦• ◦ 1.5·10−19 880 ZNF326 Zinc finger protein 326 isoform 1 DD cis 1+ 90470597 90470597 0 CCATGGATC GATCCATGG 9 17.8 ••••••••••◦◦ 7.5·10−7 −6 881 ZNF384 Zinc finger protein 384 isoform b DD cis X 12− 6781515 6781515 0 CCCCCGCCCC GGGGCGGGGG 10 28.9 •••••••◦•• ◦ 6.5·10 −7 882 ZNF384 Zinc finger protein 384 isoform b AA cis X 12− 6781698 6781698 0 GGGAGGAGGGAGG CTTCCCTCCTCTC 13 27.6 •••••••••• ◦ 2.3·10 883 ZNF384 Zinc finger protein 384 isoform b AD 12− 6787509 6781515 5994 CTCTTCCCC GGGGGAGAG 9 19.3 •••••••••• 4.3·10−7 884 ZNF384 Zinc finger protein 384 isoform b AA trans 12− 6787509 6781698 5811 TCAGCTCTT GAGAGCTGA 9 17.9 • • • • • • • ◦ • • 1.2·10−7 885 ZNF384 Zinc finger protein 384 isoform b DD trans 12− 6787828 6781515 6313 GGGGGTGGGGA TCCCCACCCCC 11 29.8 • • ◦ • • • • • • • 3.6·10−10 886 ZNF687 Zinc finger protein 687 DD cis 1+ 151254871 151254871 0 TACCCGCCC GGGCGGGTA 9 22.5 ••••••••• 5.2·10−5 887 ZNF827 Zinc finger protein 827 DA 4− 146859516 146684274 175242 TCTGCATTA TAATGCAGA 9 15.4 ••••••••• 3.7·10−2 888 ZNF827 Zinc finger protein 827 AA cis 4− 146684274 146684274 0 GTCACAGAAA TTTCTGTGAT 10 16.5 • • ◦ • • • • • • • 2.3·10−2 24 Supplementary Table 2: 10-nt seed search

No Name Gene description Arr Annot Alt Chr 5’-SS 3’-SS ∆ 5’-box 3’-box L |E| HCMCBFECLOOA P-value −5 1 ACIN1 Apoptotic chromatin condensation inducer in the DA intron X 14− 23540635 23540395 240 CCACCACCTCC GGAGGTGGTGG 11 26.3 ••••••••• 1.9·10 −6 2 ADAM22 Disintegrin and metalloproteinase AD exon X 7+ 87808249 87808357 108 TGAAATGTTT GAACATTTCA 10 13.9 • • • • • • • • • ◦ 1.7·10 3 ADAMTS6 A disintegrin and metalloproteinase with AD exon 5− 64510759 64510620 139 TGTTTTCAAT ATTGGAAACA 10 13 • • • • • • • ◦ • • 1.3·10−15 4 AFTPH Aftiphilin isoform c DD trans 2+ 64806680 64808407 1727 CTCTGCTGAT GTCAGCAGAG 10 20.1 •••••••◦•◦ • 7.7·10−13 5 AKAP9 A-kinase anchor protein 9 isoform 2 AA cis 7+ 91671359 91671359 0 CTTTTAACCCC GGGGTTAAAAG 11 19.1 ••••••••◦• ◦ 1.5·10−16 −21 6 ANK2 Ankyrin-2 isoform 2 AD exon X 4+ 114244914 114244950 36 CTAAAGTATC GATGCTTTAG 10 14.3 • • • • • • • • • ◦ 1.1·10 7 ANK3 Ankyrin-3 isoform 2 AA cis 10− 61819188 61819188 0 TTGAGGACATT AATGTCTTCAA 11 16.8 •••••••••••◦ 1.0·10−10 8 ARHGAP15 Rho GTPase-activating protein 15 AA trans 2+ 144276834 144381701 104867 TTAATGAAGC GTTTCATTAA 10 12.7 • • • • • • • • • ◦ 2.7·10−9 9 ATG4A Cysteine protease ATG4A isoform a DD trans X+ 107381114 107381221 107 CTGCTGCTCA TGAGCAGCAG 10 21.8 ••••••••• 8.6·10−12 10 ATP2B1 Plasma membrane calcium-transporting ATPase 1 AD 12− 90021493 89992366 29127 GGAAAGCTTTA TAAAGCTTTCT 11 17 •••••••••◦ ◦ 2.0·10−14 11 BAT3 Large proline-rich protein BAT3 isoform b AD exon 6− 31616741 31616687 54 CTTCTCCCAGA TCTGGGAGAAG 11 23.1 •••••••••• 1.1·10−20 12 BCOR BCL-6 corepressor isoform c AA trans X− 39930943 39923103 7840 AGTTATCTAA TTAGATGACT 10 14.4 ••••••••◦• ◦ 4.2·10−6 −21 13 BIRC3 Baculoviral IAP repeat-containing protein 3 DA intron X 11+ 102192631 102195191 2560 GTTTTGTGCAT ATGCACAAAAC 11 17.9 ••••••••• 5.2·10 14 BRD2 Bromodomain-containing protein 2 DA intron 6+ 32942542 32943160 618 GCTGCGGCCCC GGGGCCGCAGT 11 29.1 • • • • • • • • • ◦ 3.6·10−27 15 C11orf30 Protein EMSY DD cis 11+ 76250684 76250684 0 GTGCATCCATT AATGGATGCGC 11 20.3 •••••••••• 3.1·10−7 16 C12orf64 Chromosome 12 open reading frame 64 AA cis 12+ 80605728 80605728 0 GAGGAAAACA TGTTTTCTTC 10 14.5 ••◦•••••••◦◦ 7.7·10−9 17 C15orf41 Hypothetical protein LOC84529 isoform 2 AD 15+ 36936478 36983965 47487 CAGTAATTAA TTAATTACTG 10 12.8 • • ◦ • • • • • • • 3.6·10−5 18 C17orf49 MLL1/MLL complex subunit C17orf49 isoform 1 DA intron 17+ 6918197 6918380 183 GGGGTGGGGC GCCCCGCCCC 10 27.1 • • ◦ • • • • • • • 7.7·10−7 19 CADPS Calcium-dependent secretion activator 1 isoform DD cis 3− 62423778 62423778 0 CAAAATGTGAC GTCACATTTTG 11 16.9 • • • • • • • • • ◦ 1.6·10−5 −12 20 CADPS Calcium-dependent secretion activator 1 isoform DD cis X 3− 62498425 62498425 0 AGCTCCTTAA TTAAGGAGTT 10 16.1 ◦•◦••••••• • 1.8·10 21 CADPS Calcium-dependent secretion activator 1 isoform DA 3− 62522170 62502318 19852 TGATTCCTAT ATAGGAATCA 10 16.7 ••••••••◦• ◦ 1.6·10−18 25 22 CAMK2A Calcium/calmodulin-dependent protein kinase type AD 5− 149624764 149607754 17010 GCCCTGCCTG CGGGCAGGGC 10 24.4 • • ◦ • • • • • • • 2.0·10−17 23 CAMK2G Calcium/calmodulin-dependent protein kinase type DD trans 10− 75599296 75576780 22516 GCCCACTCAC GTGAGTGGGT 10 22.2 ••••◦•••••◦◦ 6.7·10−21 24 CAMSAP1L1 Calmodulin-regulated spectrin-associated protein DA intron 1+ 200822623 200823944 1321 AAGAGTCTGTTCAT ATGAACAGACTCTT 14 25 ••••◦••◦••• 3.8·10−23 −24 25 CBFA2T3 Protein CBFA2T3 isoform 1 AD exon X 16− 88964560 88964485 75 TTTTGCTTAC GTAAGTAAAA 10 12.7 ••••••••• 1.5·10 26 CCNG1 Cyclin-G1 DD cis 5+ 162864665 162864665 0 CCCTCCCCGGGCC GGCCCGGGGAGGG 13 36.7 ••••••••• 6.5·10−10 27 CDH12 Cadherin-12 preproprotein AA cis 5− 21783603 21783603 0 AATAAAGAAG CTTCTTTATT 10 12.6 •••••••••• ◦ 1.4·10−9 −10 28 CELF2 CUGBP Elav-like family member 2 isoform 2 AA cis X 10+ 11372418 11372418 0 AATGCAAATT GATTTGCATT 10 13.8 •••••••••••• 4.1·10 29 CELF2 CUGBP Elav-like family member 2 isoform 2 DA 10+ 11259470 11372418 112948 GAATCACTTT AAAGTGATTT 10 13.9 •◦◦••••••••◦ 2.4·10−17 30 CIT Citron Rho-interacting kinase DD cis 12− 120221711 120221711 0 TGTGTCTCAT ATGAGGCACA 10 18.1 ••◦••••••• ◦ 2.6·10−13 31 CLK4 Dual specificity protein kinase CLK4 AD exon 5− 178044435 178044344 91 CTCCCCGCTGA TCAGCGGGGGG 11 25.9 •••••••••••◦ 8.6·10−9 32 CNOT2 CCR4-NOT transcription complex subunit 2 DD cis 12+ 70723350 70723350 0 TGGACCAGAA TTCTGGTTCA 10 17.9 ••◦•••◦••••◦ 1.3·10−15 −12 33 COL6A3 Collagen alpha-3(VI) chain isoform 4 precursor AA cis X 2− 238296827 238296827 0 CGTGTTTCTT AAGAAACATG 10 14.3 ••••••◦••◦•• 9.4·10 34 COL7A1 Collagen alpha-1(VII) chain precursor AD 3− 48616948 48605142 11806 CTCCCTGGAG CTCCAGGGGG 10 22.2 • • • • • • • • ◦ • 9.2·10−23 35 CREBBP CREB-binding protein isoform a AA cis 16− 3801807 3801807 0 TGCTTGGGTG CACCCAAGTA 10 19.5 ••••••••••◦◦ 1.7·10−7 36 DACH1 Dachshund homolog 1 isoform c AA cis 13− 72256042 72256042 0 TTGAAACAAAT GTTTGTTTCAG 11 14.4 ••••••••••◦◦ 6.8·10−3 37 DACH1 Dachshund homolog 1 isoform c AA trans 13− 72256042 72063280 192762 TTGTTTGTTT AAACAGACAA 10 13.2 ••••••••••• 1.8·10−6 38 DDX42 ATP-dependent RNA helicase DDX42 AA trans 17+ 61876948 61877827 879 TGCAGGGAAG CTTTCCTGCA 10 18.8 ••••• ••••◦◦ 1.1·10−23 39 DDX42 ATP-dependent RNA helicase DDX42 AA cis 17+ 61876948 61876948 0 TTAGTGTTGA TCAACACTAA 10 16.2 ••••• ••••◦◦ 5.2·10−11 40 DENND1A DENN domain-containing protein 1A isoform 2 DA 9− 126554865 126433650 121215 CTGAAAGAGA TTTCTTTCAG 10 14.8 • • • • • • • • • ◦ 4.6·10−15 41 DENND1A DENN domain-containing protein 1A isoform 2 AA trans 9− 126554909 126213028 341881 ATCATCTTCT AGAAGGTGAT 10 16 • • • • • ◦ • • • • 7.1·10−4 42 EDC4 Enhancer of mRNA-decapping protein 4 AD 16+ 67912262 67916230 3968 GTCAAGTTCTG CAGAACTTGAC 11 19.4 • • ◦ • • • • • • • 2.7·10−22 43 EHBP1 EH domain-binding protein 1 isoform 2 AD 2+ 63085540 63223901 138361 CTGTTTACAG CTGTAAACAG 10 15.9 ••••••••• 8.8·10−9 −4 44 EIF4G1 Eukaryotic translation initiation factor 4 gamma AA cis X 3+ 184033276 184033276 0 GGTGGGGGGT ACCCCTCACC 10 23.3 ◦ • • • • • • • • • 3.1·10 45 EIF4G3 Eukaryotic translation initiation factor 4 gamma DD cis 1− 21205815 21205815 0 TATTCTCCCCT AGGGGAGAATA 11 22.2 • • • • • • • • • ◦ 3.6·10−13 Supplementary Table 2: (continued)

46 EPHA4 Ephrin type-A receptor 4 precursor DD trans 2− 222433437 222307548 125889 TAATGGCTTG CAAGTCATTA 10 14.5 ••••• ••••◦◦ 1.1·10−18 47 EPHA7 Ephrin type-A receptor 7 precursor AA trans 6− 94066770 93969197 97573 AAGAAAGCAT ATGCTTTCTT 10 15.9 • • ◦ • • • • • • • 5.4·10−11 48 EPHA7 Ephrin type-A receptor 7 precursor AA trans 6− 94066770 93982140 84630 GTGAAAGAAAGCA TGCTTTCTTTTAC 13 20.2 •••••••••• 2.0·10−11 −4 49 EWSR1 RNA-binding protein EWS isoform 1 AA cis X 22+ 29687550 29687550 0 AGCCAGTGCC GGTACTGGCT 10 22 ••••••••••◦◦ 8.5·10 50 EWSR1 RNA-binding protein EWS isoform 1 DD cis 22+ 29684775 29684775 0 CATTTCCATG CATGGAAATG 10 16 ••••••••••◦◦ 5.5·10−10 51 EYA4 Eyes absent homolog 4 isoform d AD 6+ 133783472 133846253 62781 CTATTTTTCTG CAGAAAAGTAG 11 14.7 •••••••••• ◦ 1.5·10−13 52 FAM98A Hypothetical protein LOC25940 DD cis 2− 33813401 33813401 0 CCTTTAGTAC GTATTAAAGG 10 14 ••◦•••••••◦◦ 1.8·10−12 53 FAP Seprase AD 2− 163039978 163029658 10320 TTAAACAAAG CTTTGTTTAA 10 12.2 • • • • • • • • • ◦ 1.0·10−12 54 FAP Seprase AA cis 2− 163029731 163029731 0 ATGTGTTGCT AGCAATACAT 10 16.3 •••••••••• ◦ 6.4·10−4 55 FAP Seprase AD exon 2− 163029731 163029658 73 CTCTGACTCTTA TAAGAGTCAGGG 12 21.2 •••••••••◦ ◦ 9.0·10−10 56 FIGN Fidgetin AD exon 2− 164591582 164591412 170 AAATTGACAT ATGTCAGTTT 10 13.7 •••••◦•••• ◦ 4.9·10−13 −7 57 FIP1L1 Pre-mRNA 3’-end-processing factor FIP1 isoform DD cis X 4+ 54306775 54306775 0 TTTCATGTTT AAACATGAAA 10 13.5 • • ◦ • • • • • • • 3.4·10 58 FOSB Protein fosB isoform 1 AA cis 19+ 45973886 45973886 0 ACACACACAT GTGTGTGTGT 10 18.6 ••••••••• 1.0·10−3 59 FOXP1 Forkhead box protein P1 isoform 2 DA 3− 71026793 71021827 4966 TTTCTATAAG CTTATAGAAA 10 13 •••••••◦•• ◦ 4.9·10−17 60 FOXP1 Forkhead box protein P1 isoform 2 AD 3− 71090683 71019886 70797 GACGGAATTAG TTAATTCCGTT 11 16.4 •••••••••• ◦ 1.0·10−15 61 FOXP2 N/A AD 7+ 114284739 114294064 9325 TTTTCTGACTG CAGTTAGAAAA 11 15.9 ••◦••••••• ◦ 2.1·10−10 62 FTSJ3 Putative rRNA methyltransferase 3 AD 17− 61902097 61901690 407 CTTCCTCTCC GGAGAGGAAG 10 21 ••◦••••••• ◦ 8.4·10−28 63 GAPVD1 GTPase-activating protein and VPS9 DA intron 9+ 128104578 128109097 4519 AGAGCACATATTTC GAGATATGTGCTCT 14 24.2 ••◦••••••• ◦ 2.7·10−13 64 GLCCI1 Glucocorticoid-induced transcript 1 protein DD cis 7+ 8124647 8124647 0 TGTCAGCTGG CCAGCTGATA 10 19.9 •••••••••◦ • 6.7·10−13 −12 65 GPR162 Probable G-protein coupled receptor 162 isoform DD cis X 12+ 6932929 6932929 0 CCCCCACCCCC GGGGGTGGGGG 11 30.7 • • • • • • • • ◦ • 1.4·10 −6 66 GRIA3 Glutamate receptor 3 isoform 2 precursor AD exon X X+ 122599524 122599639 115 TCTTGTGCTC GAGCACAAGA 10 19.7 ••••••••◦• ◦ 2.0·10 −3

26 67 GRIA3 Glutamate receptor 3 isoform 2 precursor DD cis X+ 122598963 122598963 0 GTGGGTGGAATA TATTCCACCTAC 12 21.9 •••••••••• 3.9·10 68 GRIK2 Glutamate receptor, ionotropic kainate 2 isoform DD cis 6+ 102337738 102337738 0 TTTTGGCAATT AATTGTCAAAA 11 13.8 •••••••••• 3.2·10−8 69 GTDC1 Glycosyltransferase-like domain-containing AD exon 2− 144709640 144709548 92 GACTAATATC GATATTAGTT 10 13.7 ••◦••••••••◦ 8.8·10−9 70 HDAC1 Histone deacetylase 1 DA intron 1+ 32792678 32793136 458 GCCAGGTTCC GGGACCTGGC 10 22.5 ◦••••••••• ◦ 4.7·10−15 71 HECW1 E3 ubiquitin-protein ligase HECW1 DD cis 7+ 43283531 43283531 0 CATTCCATTA TAATGGAATG 10 15.2 ••••••••• 1.3·10−7 72 HIVEP1 Zinc finger protein 40 DD cis 6+ 12130125 12130125 0 AAATGTACATTTA TAAATGTACATTT 13 17 ••◦••••••• ◦ 1.9·10−14 73 HNRNPD Heterogeneous nuclear ribonucleoprotein D0 AD 4− 83292737 83277948 14789 TTTTGATTGG CCAGTCAAAA 10 14.6 ••••••••• 4.6·10−8 74 HNRNPH1 Heterogeneous nuclear ribonucleoprotein H DA 5− 179048242 179046408 1834 AATTTTAGGT ACCTAAAGTT 10 13.6 ••••• ••••◦◦ 2.4·10−14 75 HNRNPK Heterogeneous nuclear ribonucleoprotein K AA trans 9− 86588888 86588314 574 TAGCTTTACCA TGGTAAAGTTA 11 17.2 •••••••••• 1.0·10−12 76 HNRNPM Heterogeneous nuclear ribonucleoprotein M DA 19+ 8527465 8548041 20576 GAAATCAGGAAGG TCTTCCTGATTTC 13 22.1 •••••••••• 3.6·10−14 77 HOXC6 Homeobox protein Hox-C4 AD exon 12+ 54447700 54448145 445 CAGGGTCGCT AGCGACTCTG 10 20.3 ••••••••◦• ◦ 9.4·10−10 78 HOXC6 Homeobox protein Hox-C4 AD 12+ 54422359 54448145 25786 AAAGGCAAAG CTTTGCTTTT 10 13.9 •••••••••◦ ◦ 9.9·10−9 79 HUWE1 E3 ubiquitin-protein ligase HUWE1 DD trans X− 53590706 53578226 12480 TTGCTCAGCTCT AGAGCTGAGCAG 12 24.8 ••◦••••••• ◦ 1.1·10−19 80 IKZF2 Zinc finger protein Helios isoform 1 AD 2− 214014971 214014904 67 GGGAAAGAGA TCTCTTTCTC 10 16.8 • ◦ • • • • • • • • 1.1·10−10 81 ILDR2 Immunoglobulin-like domain-containing receptor AA cis 1− 166904714 166904714 0 TTGTGGAGGG CCCTCCACAG 10 21.4 •••••••◦•• ◦ 9.7·10−17 −7 82 ILF3 Interleukin enhancer-binding factor 3 isoform d AA cis X 19+ 10795091 10795091 0 GGAGCAGAGA TCTCTGCTCT 10 21.1 ••◦•••••◦• • 1.2·10 83 ILKAP Integrin-linked kinase-associated DA intron 2− 239098493 239096898 1595 CCCAGAGCAA TTGCTCTGGG 10 21.7 ••••••• ◦••◦ 2.4·10−30 84 INPP4B Type II inositol-3,4-bisphosphate 4-phosphatase AA cis 4− 142950067 142950067 0 AATGTAGAGTTG CAACTCTGCATT 12 19.4 ••••••••••• 4.2·10−5 85 IQCH IQ domain-containing protein H isoform 1 AA cis 15+ 67709268 67709268 0 CCACAAGCAGTTTT AAAATTGCTTGTGG 14 22.9 •••••••••••◦ 6.9·10−7 86 IQCH IQ domain-containing protein H isoform 1 DD trans 15+ 67665000 67681344 16344 AGCTGTTAAG TTTAACAGCT 10 15.6 ••••••• •◦•◦ 1.8·10−22 87 KAT5 Histone acetyltransferase KAT5 isoform 3 DA 11+ 65480305 65481063 758 GAGCGGCTGG CCAGCCGCTC 10 24.5 •••••••••• 3.2·10−13 88 KCNC1 Potassium voltage-gated channel subfamily C DA intron 11+ 17801191 17803216 2025 GTATGTAGAG CTTTACATAC 10 14.2 • • • ◦ • • • • • • 9.9·10−15 89 KIAA0913 Hypothetical protein LOC23053 DA 10+ 75549297 75556870 7573 GTGAGGCCCTC GAGGGCTTCAC 11 23.9 ••••••••◦• ◦ 5.7·10−21 90 KIAA0913 Hypothetical protein LOC23053 DA 10+ 75556772 75560774 4002 GGGCAGGGGGG TCCCCCTGCCC 11 28.9 • • ◦ • • • • • • • 1.0·10−11 91 KIAA1409 Protein unc-79 homolog AA cis 14+ 93940593 93940593 0 GCACAGGGAA TTTCCTGTGC 10 18.9 • • ◦ • • • • • • • 1.7·10−2 Supplementary Table 2: (continued)

92 KIAA1468 Hypothetical protein LOC57614 AA trans 18+ 59888269 59947592 59323 TTTCTTGGTT AACCAAGAAA 10 15.7 ••◦••••••• ◦ 1.2·10−8 93 KIF1B Kinesin-like protein KIF1B isoform b AA cis 1+ 10342457 10342457 0 GATTTTCAGA TCTGAGAATC 10 15.3 • • • • • • • • • ◦ 1.4·10−5 −22 94 KIF21A Kinesin-like protein KIF21A isoform 1 DA intron X 12− 39724547 39724064 483 GAATAGATGCT GGCATCTATTC 11 18.9 ••••••••••• 6.5·10 95 KPNA3 Importin subunit alpha-3 DA intron 13− 50296612 50296260 352 CTATGTTTCCTC GAGGAAACATAG 12 20.8 •••••••••• 5.7·10−19 96 KPNB1 Importin subunit beta-1 DD trans 17+ 45727650 45727810 160 GGGGGAGGGG CCCCTCCCCC 10 27.6 ••••••◦••• • 1.0·10−18 97 LRPPRC Leucine-rich PPR motif-containing protein, AA trans 2− 44171033 44132919 38114 CGTTTAGAAA TTTCTAAATG 10 12.2 • • • • • • • • • ◦ 5.9·10−3 98 LRPPRC Leucine-rich PPR motif-containing protein, AA trans 2− 44175657 44171033 4624 AATTTTAGTG CACTAGAATT 10 12.5 ••••• •••••◦ 4.6·10−5 99 MAP2K5 Dual specificity mitogen-activated protein AA cis 15+ 67879183 67879183 0 CTAATTAACC GGTTAATTAG 10 14 •◦◦•••••◦••• 2.0·10−15 100 MAP2K5 Dual specificity mitogen-activated protein AA trans 15+ 68040568 68040906 338 AATGCAATAA TTATTGCATT 10 13.8 •••••••••••◦ 8.4·10−7 101 MAP2K5 Dual specificity mitogen-activated protein DA 15+ 67873161 68040906 167745 TAATCAACAAT GTTGTTGATTA 11 15.3 ••••••••••◦◦ 2.4·10−12 102 MAP2K5 Dual specificity mitogen-activated protein DA 15+ 67878268 67893022 14754 GAAATGTCAA TTGACATTTC 10 15 •••••••••••◦ 5.3·10−10 103 MAP2K6 Dual specificity mitogen-activated protein DD cis 17+ 67411141 67411141 0 AAAAATGCAA TTGCATTTTT 10 13.2 ◦••••••••• ◦ 2.7·10−5 104 MBNL1 Muscleblind-like protein 1 isoform e AA trans 3+ 152174055 152175918 1863 CTTCTGTATG CATGCAGAAG 10 16.3 ••••••••◦• ◦ 6.2·10−7 105 MCTP1 Multiple C2 and transmembrane domain-containing DA 5− 94207019 94114868 92151 TCTGTCATTT AAATGACAGA 10 16.2 •••••••••◦ ◦ 6.1·10−18 −7 106 MDM4 N/A DD cis X 1+ 204506625 204506625 0 TGGACTCCCAAGA TCTTGGGAGTTCA 13 25.7 •••••••••••• 4.5·10 107 MECOM MDS1 and EVI1 complex locus protein EVI1 isoform DD cis 3− 168830574 168830574 0 TAGGATTTCCT AGGAAATTCTA 11 16.9 ••◦•••••••◦◦ 8.2·10−10 −8 108 MECP2 Methyl-CpG-binding protein 2 isoform 2 DD cis X X− 153357641 153357641 0 TTCCTTTTTTTT AAAAAAAAGGAA 12 15 •••••••••• 5.9·10 −12 109 MED23 Mediator of RNA polymerase II transcription DA intron X 6− 131937046 131936481 565 GCAAAACAGT ACTGTTTTGT 10 15.9 ••◦••••••• • 3.2·10 −2 110 MEF2A Myocyte-specific enhancer factor 2A isoform 2 DD cis X 15+ 100211659 100211659 0 TCCTTTTTGTT AACAAGAAGGA 11 16.7 ••••••••••◦◦ 2.2·10 111 MEF2C Myocyte-specific enhancer factor 2C isoform 4 DD trans 5− 88057085 88056804 281 ATCAGCAGGC GTCTGCTGAT 10 19.3 •••••••••••• 4.4·10−17 112 MEF2C Myocyte-specific enhancer factor 2C isoform 4 AA trans 5− 88057145 88018646 38499 AGGTTTGAACT AGTTCAAATCT 11 16.5 ••••••••••◦◦ 9.9·10−17 −3

27 113 MGEA5 Bifunctional protein NCOAT isoform b DD cis 10− 103553669 103553669 0 AACTGAATTGA TCAATTTAGTT 11 14.9 •••••••••••◦ 2.6·10 114 MGEA5 Bifunctional protein NCOAT isoform b AD exon 10− 103553755 103553669 86 TTTCTCGTAA TTATGAGAAA 10 13.7 ••••••◦••••◦ 8.2·10−12 115 MSI2 RNA-binding protein Musashi homolog 2 isoform b DA intron 17+ 55729522 55752332 22810 CCAGGCATGC GCATGCCTGG 10 22.9 •••••••••• ◦ 1.9·10−16 116 MYCBP2 Probable E3 ubiquitin-protein ligase MYCBP2 AD exon 13− 77807398 77807290 108 TTTCTCCTCAG CTGAGGAGAAA 11 20.7 ••••• ••••◦◦ 2.5·10−19 117 MYH7B Myosin-7B AD 20+ 33565434 33588696 23262 TTGTGTCCTG CAGGACACAA 10 19.4 • • • • • • • • • ◦ 2.3·10−18 118 MYL6B Myosin light chain 6B AA trans 12+ 56547656 56548596 940 GCCAACTGGC GCCAGTTGGT 10 21.9 •••••••••◦◦ 4.4·10−19 119 MYNN Myoneurin isoform B AA trans 3+ 169496671 169501264 4593 AGATGGAAGA TTTTCCATCT 10 16.2 ••◦•• •••••◦ 2.4·10−15 120 NEB Nebulin isoform 2 DA 2− 152544139 152359399 184740 TACAAGAAAG CTTTCTTGTA 10 14.9 • • • • • • • • • ◦ 5.5·10−26 121 NEB Nebulin isoform 2 DA 2− 152551035 152359399 191636 TACAAGAAAG CTTTCTTGTA 10 14.9 • • • • • • • • • ◦ 1.6·10−26 −9 122 NFIB Nuclear factor 1 B-type isoform 2 DD cis X 9− 14116206 14116206 0 AAATGAGAAAT ATTTCTCATTT 11 14.8 •••••••••• ◦ 4.1·10 123 NFIB Nuclear factor 1 B-type isoform 2 DA 9− 14179725 14113080 66645 GGAGAACAAA TTTGTTCTTC 10 14.3 • • • • • • • • • ◦ 7.1·10−14 124 NFYC Nuclear transcription factor Y subunit gamma DA 1+ 41157539 41236380 78841 GGGGGAGGGGC GCCCCTCTCCC 11 28 • • ◦ • • • • • • • 6.5·10−20 125 NLGN3 Neuroligin-3 isoform 2 AD X+ 70367399 70368755 1356 TCCCTCTTTC GAGAGAGGGA 10 19.9 • • • • • • • • • ◦ 3.0·10−20 −10 126 NLGN3 Neuroligin-3 isoform 2 DA intron X X+ 70368755 70373326 4571 AGAGAGAGAG TTCTCTCTCT 10 18.6 • • • • • • • • • ◦ 6.2·10 127 NR2E1 Nuclear receptor subfamily 2 group E member 1 AA trans 6+ 108501526 108502010 484 TATTGTATGA TCATACAATA 10 14.5 ••••••••◦• ◦ 2.4·10−12 128 NRXN1 Neurexin-1-beta isoform alpha2 precursor AA trans 2− 50755789 50282182 473607 ATTTTATTGG CCAATGAAAT 10 12.6 •••••••••• 2.9·10−5 129 NRXN1 Neurexin-1-beta isoform alpha2 precursor DA 2− 50848363 50755789 92574 CTGTAGACATC GATGTCTGCAG 11 20 ••••••••••• 6.5·10−6 130 NRXN2 Neurexin-2-beta isoform alpha-2 precursor DD cis 11− 64387765 64387765 0 CCCCCCTCCC GGGAGGGGGG 10 27.6 • • • • • • • ◦ • • 2.4·10−10 131 NRXN2 Neurexin-2-beta isoform alpha-2 precursor AD 11− 64457948 64427803 30145 GCTTCTCCAG CTGGAGAAGC 10 20.8 •••••••••• 2.6·10−19 132 NT5C2 Cytosolic purine 5’-nucleotidase DD trans 10− 104860991 104860801 190 AGAGACCTAC GTAGGTCTTT 10 17.5 •••••••••• ◦ 4.1·10−18 133 NTNG1 Netrin-G1 isoform 3 AD 1+ 107973371 107979421 6050 TTTCTGTTCT AGAGCAGAAA 10 16 ••••••••◦• ◦ 8.4·10−20 −6 134 NTNG1 Netrin-G1 isoform 3 DD cis X 1+ 107963765 107963765 0 GATTCATACAGTG CACTGTATGAATC 13 22 ••••••••••• 3.6·10 −13 135 PAPD5 PAP-associated domain-containing protein 5 DA intron X 16+ 50258905 50259149 244 ACGTTTTCCAA TTGGAAAATGT 11 16.4 •••••••••• ◦ 1.1·10 −7 136 PCBP2 Poly(rC)-binding protein 2 isoform e AD exon X 12+ 53858543 53858636 93 TGGAGACTGAA TTCAGTCTCCA 11 22 ••••••••• 1.5·10 137 PCDH8 Protocadherin-8 isoform 1 precursor DD cis 13− 53420231 53420231 0 CCCGGCTCCCC GGGGAGCCGGG 11 30.1 ••◦•••••••◦◦ 3.5·10−8 Supplementary Table 2: (continued)

138 PCGF5 Polycomb group RING finger protein 5 AD exon 10+ 93031394 93031454 60 TGCCTCTTAT GTAAGAGGCA 10 19 •••••••••••• 1.9·10−26 139 PHF1 PHD finger protein 1 isoform b DD trans 6+ 4862852 4863167 315 GGGGCTGGGGGG TCCCCCAGCCCT 12 31 •••••••••• 2.5·10−14 140 POLD3 DNA polymerase delta subunit 3 DD cis 11+ 74324055 74324055 0 CTAGTAAAAC GTTTTATTAG 10 11.6 ••••••••◦•◦ 2.6·10−10 141 PPIP5K2 Inositol hexakisphosphate and DA intron 5+ 102515889 102518934 3045 GAAAATACAG CTGTATTTTT 10 12.8 ••••• •••••◦ 4.5·10−21 142 PPP1R12A Protein phosphatase 1 regulatory subunit 12A DA intron 12− 80199945 80199548 397 TGGATTTTTT AAAAAATCCA 10 13.4 ••••••••••• 6.8·10−18 143 PRPF39 Pre-mRNA-processing factor 39 DD cis 14+ 45565431 45565431 0 TAGGTACTGT GCAGTACCTA 10 19.1 •••••••••◦◦◦ 1.6·10−14 144 PSMD11 26S proteasome non-ATPase regulatory subunit 11 DA 17+ 30781637 30807770 26133 GTCAGTTTCT AGAAACTGAC 10 17.3 •••••••••• 1.2·10−20 145 PSMD14 26S proteasome non-ATPase regulatory subunit 14 AA trans 2+ 162175332 162241974 66642 TTTGTTTCTG CAGAAACAGA 10 14.6 ••••••••• 3.2·10−8 146 PTBP2 Polypyrimidine tract-binding protein 2 DD trans 1+ 97272008 97278484 6476 TCTTTTGCTA TAGCAGAAGA 10 16.2 ••••••••••◦◦ 2.1·10−19 147 PTPRD Receptor-type tyrosine-protein phosphatase delta DA 9− 8527344 8521546 5798 ATGGCATGCA TGCATGTCAT 10 18 •••••••••◦ ◦ 4.9·10−18 −6 148 PTPRD Receptor-type tyrosine-protein phosphatase delta AD exon X 9− 8523524 8523512 12 TCATTTCATT AATGAAATGA 10 13.9 ••••••••••• 1.3·10 149 PTPRD Receptor-type tyrosine-protein phosphatase delta DA 9− 8523512 8499840 23672 GAATACAAAT GTTTGTATTC 10 13.2 ••◦•••••◦• • 1.2·10−14 150 PUM2 Pumilio homolog 2 AA cis 2− 20478580 20478580 0 ATCACAGTAATT AATTATTGTGAT 12 16.1 •••••••••• 1.1·10−5 151 QKI Protein quaking isoform HQK-5 AA cis 6+ 163991725 163991725 0 GATTAGTTTT GAAACTAATC 10 13.1 •••••••••••• 1.9·10−7 152 RAPGEF4 Rap guanine nucleotide exchange factor 4 isoform DA 2+ 173855653 173885345 29692 CTAATCACAC GTGTGATTAG 10 16.4 • • • • • • • ◦ • • 7.7·10−13 153 RAPGEF4 Rap guanine nucleotide exchange factor 4 isoform DA 2+ 173855653 173901355 45702 TACAATAGCA TGCTATTGTG 10 16.2 ••••••••• 1.0·10−10 −7 154 RBBP6 E3 ubiquitin-protein ligase RBBP6 isoform 2 AA cis X 16+ 24579112 24579112 0 GGAAAACTAA TTAGTTTTCT 10 13.7 •••••••◦••◦◦ 1.5·10 155 RBFOX1 Fox-1 homolog A isoform 1 DA 16+ 7714970 7721558 6588 CAAGTTTGCT AGCAAACTTG 10 16.7 •••••••••• 2.1·10−21 156 RBFOX1 Fox-1 homolog A isoform 1 DA intron 16+ 7637302 7645550 8248 GGGAAACAAC GTTGTTTTCC 10 15.3 ••◦•• •••••◦ 9.7·10−19 157 RBFOX3 Fox-1 homolog C AA cis 17− 77092774 77092774 0 GGAGCAAACG CGTTTGCTTC 10 16.8 • • • • • • • • • ◦ 1.7·10−4 158 RBM39 RNA-binding protein 39 isoform a AD 20− 34317287 34300940 16347 AGGAAAGATT AATCTTTTCT 10 13.2 ••◦•••••••◦ 6.5·10−19 −24

28 159 REPS1 RalBP1-associated Eps domain-containing protein DA 6− 139265634 139237113 28521 GTGACATTTT AAAATGTCAT 10 14 ••◦••••••• ◦ 6.1·10 160 RERE Arginine-glutamic acid dipeptide repeats protein DA intron 1− 8674619 8617582 57037 AAGGAGAATC GATTTTCCTT 10 15 •••••••••• 3.0·10−14 161 RPGRIP1L Protein fantom isoform a DA 16− 53730062 53698921 31141 AAAAGCTTTTAG CTAAAAGCTTTT 12 16.4 ••••••••••◦ 4.2·10−16 162 RUNX1T1 Protein CBFA2T1 isoform B AD 8− 93088365 92988132 100233 TTGTTGTTGT ACAACAACAA 10 15.6 ••••••◦••• ◦ 3.3·10−21 163 SEZ6L2 Seizure 6-like protein 2 isoform 3 DA 16− 29910261 29884064 26197 TGGGGAAGGG CTCTTCCCCA 10 21 • • • • • • • • • ◦ 3.4·10−22 164 SF1 Splicing factor 1 isoform 5 DA 11− 64540901 64535316 5585 CTGGTGGCAACAT ATGTTGCCACTAG 13 24.6 ••••••••••◦ 2.2·10−23 165 SF1 Splicing factor 1 isoform 5 DA 11− 64540901 64534551 6350 TTACCTTTTT GAAAAGGTAA 10 13.8 •••••••• •◦◦ 1.9·10−24 166 SF1 Splicing factor 1 isoform 5 AA trans 11− 64537880 64532990 4890 AGGCAGAGGG CCCTTTGCCT 10 21.5 • • • • • • • • ◦ • 2.3·10−12 167 SF1 Splicing factor 1 isoform 5 DA intron 11− 64535577 64535316 261 TGGCAACATTGTTCTT AAGAACAATGTTGCCA 16 28.7 •••••••••• 1.0·10−21 168 SHC1 SHC-transforming protein 1 isoform 1 AA trans 1− 154942675 154941310 1365 GGGGAGGGGA TCCCCTCCCC 10 26.7 •••••••••• 8.4·10−15 169 SIK3 Serine/threonine-protein kinase SIK3 DD cis 11− 116741046 116741046 0 TCCTTGGGCAG CTGCCCAAGGA 11 25 ◦•••••••••◦◦ 1.1·10−12 −6 170 SLC8A1 Sodium/calcium exchanger 1 isoform B DD cis X 2− 40404891 40404891 0 GTGTGAGAGTA TACTCTCACAC 11 21.1 • • • • • • • • • ◦ 1.6·10 171 SMARCE1 SWI/SNF-related matrix-associated AD 17− 38802099 38798706 3393 TTGATTCTCTT AGGAGAATCAA 11 17 • • • • ◦ • • • • • 3.0·10−17 172 SMARCE1 SWI/SNF-related matrix-associated DD trans 17− 38802047 38798706 3341 TCAGTTGTTT AAACAACTGG 10 14.9 •••••••◦••◦◦ 1.0·10−18 173 SMG7 Protein SMG7 isoform 2 AD 1+ 183486822 183511499 24677 CTTTCTTGTT AACAGGAAAG 10 14.2 • • • • • • • • • ◦ 3.5·10−11 174 SNRNP200 U5 small nuclear ribonucleoprotein 200 kDa AA trans 2− 96944449 96940893 3556 CTGCAGGGTC GACCTTGCAG 10 20.3 • • • • • • • • ◦ • 8.6·10−23 175 SORBS2 Sorbin and SH3 domain-containing protein 2 AA trans 4− 186696520 186508842 187678 CTGAAAATAG CTATTTTCAG 10 13.8 •••••••••◦ ◦ 1.4·10−26 176 SOX2OT N/A DD cis 3+ 181328717 181328717 0 TAATTGACTTG CAAGTCAATTG 11 15.7 ••••••••••◦◦ 2.7·10−11 177 SRSF1 N/A AA cis 17− 56081362 56081362 0 TTTTGGGGAAT ATTCCCCAGAA 11 19.2 •••••••••••◦ 2.3·10−4 −4 178 SRSF3 N/A AA cis X 6+ 36567597 36567597 0 TGAAAAACAA TTGTTTTTCA 10 13.3 •••••••◦•• ◦ 2.5·10 −2 179 SRSF6 Serine/arginine-rich splicing factor 6 DD cis X 20+ 42088060 42088060 0 GTTAAGTTTT AAAACTTAGC 10 12.3 •••••••••••• 7.6·10 180 SRSF7 Serine/arginine-rich splicing factor 7 isoform DD trans 2− 38973835 38973285 550 TCCAAAGAGTTCAAAG CTTTGAGCTCTTTGGA 16 27.7 •••••••••••◦ 9.0·10−26 181 STRN Striatin DD cis 2− 37113858 37113858 0 GGAAAACATTG CAATGTTTTCC 11 16.8 ••••••••••• 1.5·10−7 −13 182 SYNJ1 Synaptojanin-1 isoform c DD cis X 21− 34007170 34007170 0 TAGATGTATG CATACATCTA 10 15.7 ••••••••◦•◦◦ 1.1·10 183 TAOK2 Serine/threonine-protein kinase TAO2 isoform 1 DA intron 16+ 29997825 30000913 3088 GAGGAGGAGGAA TTCCTCCTCTTC 12 24 •••••••••• ◦ 5.8·10−21 Supplementary Table 2: (continued)

184 TCF4 Transcription factor 4 isoform a AA cis 18− 52928764 52928764 0 TTAATGCTAATTA TAATTAGCATTAA 13 17.3 ••••••••••◦◦ 5.2·10−5 185 TCF4 Transcription factor 4 isoform a AD 18− 53070749 52899751 170998 CTGTTACCTG TAGGTAACAG 10 17.2 •••••••••••◦ 2.6·10−17 186 TCF7L2 Transcription factor 7-like 2 isoform 7 AD 10+ 114724314 114920450 196136 GCTTTGATTT AAATCAAAGC 10 14.7 • • ◦ • • • • • • • 2.2·10−12 187 THOC2 THO complex subunit 2 DA intron X− 122754757 122753287 1470 TAGAAAATGAA TTCATTTTCTA 11 15 •••••••••• ◦ 1.2·10−10 188 TLE1 Transducin-like enhancer protein 1 DA 9− 84268888 84228436 40452 TTTATCACAA TTGTGATAAA 10 13.9 ••◦••••••• ◦ 1.0·10−8 189 TLE1 Transducin-like enhancer protein 1 AA trans 9− 84300811 84268951 31860 AAGGACAAAG CTTTGTCTTT 10 14.2 ••◦••••••• ◦ 3.6·10−22 190 TM9SF4 Transmembrane 9 superfamily member 4 precursor DA 20+ 30729468 30738602 9134 CCCGGCTGGA TCCAGCCGGG 10 25.6 •••••••◦•• ◦ 1.1·10−23 191 TNRC6A Trinucleotide repeat-containing gene 6A protein AD 16+ 24804793 24807260 2467 CTTTCTAAAG CTTTAGAAAG 10 13.6 • • • • • • ◦ • • • 4.7·10−16 192 TOP2B DNA topoisomerase 2-beta DD trans 3− 25660144 25659908 236 AATAGAAGAC GTCTTCTGTT 10 15.4 • • ◦ • • • • • • • 2.2·10−12 −8 193 TRIM33 E3 ubiquitin-protein ligase TRIM33 isoform beta AA cis X 1− 114940612 114940612 0 TAGAAAGGAT ATCCTTTTTA 10 13.9 ••◦•• •••••• 1.9·10 194 TRPM1 Transient receptor potential cation channel DD cis 15− 31323185 31323185 0 TCCAAATTAAT ATTAATTTGGA 11 14.9 ••••••••◦•◦• 6.1·10−16 195 TTN Titin isoform N2-A AD 2− 179622643 179517184 105459 TTCTTTTCAG CTGAAAAGAA 10 14.7 •••••••••• ◦ 4.8·10−29 196 TTN Titin isoform N2-A AD 2− 179544143 179485441 58702 CAATATCTTT AAAGATATTG 10 12.8 ••••••••◦• ◦ 4.8·10−26 197 TTN Titin isoform N2-A DD trans 2− 179483310 179472511 10799 TGACAGAAACA TGTTTCTGTCA 11 19.4 •••••••••• ◦ 1.0·10−24 198 TTN Titin isoform N2-A AA trans 2− 179622643 179523815 98828 TTCTTTTCAG CTGAAAAGAA 10 14.7 •••◦•••••• ◦ 1.8·10−29 199 UBAP2L Ubiquitin-associated protein 2-like isoform a DD cis 1+ 154214041 154214041 0 TTCTATCCCT AGGGATAGAA 10 18.9 •••••••◦•• ◦ 2.0·10−11 200 UBR4 E3 ubiquitin-protein ligase UBR4 DA intron 1− 19467840 19467386 454 ACAGGTGGAGA TCTCCACTTGT 11 21.5 •••••◦•••• ◦ 4.1·10−24 201 UBR4 E3 ubiquitin-protein ligase UBR4 DA 1− 19499674 19468018 31656 ACCACCATCT AGATGGTGGT 10 20.8 ••◦••••••• ◦ 4.1·10−25 202 VAMP4 Vesicle-associated membrane protein 4 isoform 1 DD cis 1− 171673526 171673526 0 TTCAAATTGGA TCTAATTTGAA 11 14.7 • ◦ • • • • • • • • 3.6·10−10 −3 203 WNK3 Serine/threonine-protein kinase WNK3 isoform 1 DD cis X X− 54265441 54265441 0 AAAAAGCTGG CCAGCTTTTT 10 16.6 ••••••••• 5.6·10 204 WSB1 WD repeat and SOCS box-containing protein 1 DA intron 17+ 25633908 25636125 2217 TGCTCGGTGTC GACACTGAGCA 11 22.4 • • • • • • • • • ◦ 7.5·10−16 −9

29 205 ZEB2 N/A DD cis 2− 145162402 145162402 0 CCTCTGCAGCTGTT AACAGCTGCAGAGG 14 30.3 •••••••◦••◦• 4.5·10 206 ZEB2 N/A DD trans 2− 145161482 145153978 7504 ATTTCTTTCT AGGAAGAAAT 10 13.2 •••••••••◦ • 5.5·10−10 −16 207 ZFX Zinc finger X-chromosomal protein isoform 3 AD exon X X+ 24227016 24227216 200 GTCATTCATGAGTATCA TGATATTCATGAATGAT 17 26.9 •••••••••• 2.2·10 −8 208 ZNF384 Zinc finger protein 384 isoform b DD cis X 12− 6781515 6781515 0 CCCCCGCCCC GGGGCGGGGG 10 28.9 •••••••◦•• ◦ 1.3·10 −10 209 ZNF384 Zinc finger protein 384 isoform b AA cis X 12− 6781698 6781698 0 GGGAGGAGGGAGG CTTCCCTCCTCTC 13 27.6 •••••••••• ◦ 3.5·10 210 ZNF384 Zinc finger protein 384 isoform b DD trans 12− 6787828 6781515 6313 GGGGGTGGGGA TCCCCACCCCC 11 29.8 • • ◦ • • • • • • • 2.5·10−13 211 ZNF827 Zinc finger protein 827 AA cis 4− 146684274 146684274 0 GTCACAGAAA TTTCTGTGAT 10 16.5 • • ◦ • • • • • • • 2.4·10−7