Table S2. Baseline characteristics of the Rotterdam Study for interaction analysis

Transcription

1 Supplementary data Table S1. List of the primers for the cloning of precursor mir-4707 Table S2. Baseline characteristics of the Rotterdam Study for interaction analysis Table S3. List of the primers for the cloning of 3 UTR sequence of CARD10 Table S4. List of databases and web tools used for functional annotation of mirna-binding site SNPs associated with POAG endophenotypes Table S5. MiRNA genetic variants nominally associated with POAG endophenotypes Table S6. mir-612 and mir p putative target genes associated with and cup area Table S7. Expression of the putative mir-612 and mir p target genes associated with and cup area across different eye tissues Table S8. The mirna-target gene interaction analysis using the Rotterdam Study data Table S9. Forty-seven mirna-binding site variants within the 3 UTRs of 21 genes associated with POAG endophenotypes Table S10. Functional characteristics of 47 mirna-binding site variants associated with POAG endophenotypes Table 11. Expression of genes hosting the 47 mirna-binding site variants associated with POAG endophenotypes across eye tissues Table S12. Prioritization of 47 mirna-binding site variants associated with POAG endophenotypes Figure S1. The predicted hairpin structure of pre-mir-612 and pre-mir-4707 and the position of two identified variants associated with and cup area Figure S2. Manhattan plots showing the association of 72,052 mirna-binding site variants with POAG endophenotypes Figure S3. Regional plots showing the association of ten highlighted mirna-binding site variants with POAG endophenotypes

2 Table S1. List of the primers for the cloning of precursor mir-4707 Oligo name Sequence (5'-3') mir-4707_wt_f mir-4707_wt_r mir-4707_mut_f mir-4707_mut_r 5 TCGAGGGTTCCGGAGCCCCGGCGCGGGCGGGTTCTGGGGTGTAGACGCTGC TGGCCAGCCCGCCCCAGCCGAGGTTCTCGGCACCG 3 5 AATTCGGTGCCGAGAACCTCGGCTGGGGCGGGCTGGCCAGCAGCGTCTACA CCCCAGAACCCGCCCGCGCCGGGGCTCCGGAACCC 3 5 TCGAGGGTTCCGGAGCCCCGGCGCGGGCGGGTTCTGGGGTGTAGACGCTGC TGGCCAGCCCUCCCCAGCCGAGGTTCTCGGCACCG 3 5 AATTCGGTGCCGAGAACCTCGGCTGGGTAGGGCTGGCCAGCAGCGTCTACA CCCCAGAACCCGCCCGCGCCGGGGCTCCGGAACCC 3 WT, Wild type pre-mirna sequence containing allele G at the rs SNP site; Mut, Mutant premirna containing allele A at the rs SNP site; F, Forward; R, Reverse. The restriction enzymes XhoI and EcoRI (with sticky end) are shown in red and the position of SNP is underlined in the pre-mirna sequence.

3 Table S2. Baseline characteristics of the Rotterdam Study for interaction analysis Total Number of participants 10,404 Age (years) 64.4 (9.1) Sex (male) 4441 (42.7 %) Body mass index (kg/m 2 ) (9.14) Systolic blood pressure (mmhg) (25.66) Diastolic blood pressure (mmhg) (18.46) Data are mean (SD) or n (%)

4 Table S3. List of the primers for the cloning of 3 UTR of CARD10 gene Oligo name Sequence (5'-3') CARD10_F CARD10 _R 5 CTAGATGTAAATGTCACGCCCCACCCCTGTTTCATGTGGGCACTAACAC GTGTGCGTTCCTGGCGGGCACACTCAGGACGGGCC 3 5 CGTCCTGAGTGTGCCCGCCAGGAACGCACACGTGTTAGTGCCCACATGA AACAGGGGTGGGGCGTGACATTTACAT 3 F, Forward; R, Reverse. The restriction enzymes XbaI and ApaI (sticky end) are shown in red and the binding site of mir p within the 3 UTR of CARD10 is underlined.

5 Table S4. List of databases and web tools used for functional annotation of mirna-binding site SNPs associated with POAG endophenotypes Name Main feature URL mirnasnp v2 SNPs in mirna-related sequences PolymiRTS 3.0 SNPs in mirna binding sites Vienna RNA Prediction of SNP effect on mirna secondary structure TargetScan 7.0 mirna target prediction mirdb mirna target prediction / IPA A comprehensive software on biological and pathway analysis OTDB Gene expression data across different human eye tissues from the Ocular Tissue Database HMDD The human mirna expression database SNAP Proxy SNPs based on linkage disequilibrium and physical distance HaploReg v4.1 For exploring annotations of variants on haplotype blocks Genenetwork Whole blood eqtl data GTEx eqtl data in other tissue mirbase mirna information GeneCards LocusZoom A database of human genes Generating regional association plots

6 Table S5. MiRNA genetic variants nominally associated with POAG endophenotypes mirna ID Location SNP ID A1 A2 Freq A1 Chr Effect P-value Pheno in mir mir-1178 seed rs t c DA mir-1178 premir rs a g mir-1208 premir rs t g mir-1208 premir rs c g IOP mir-1258 premir rs t c mir-1269b seed rs c g CA mir-1269b seed rs c g mir premir rs a g CA mir-1343 premir rs t c DA mir-199b premir rs t c CA mir-300 premir rs t c DA mir-3144 mature rs a g CA mir-3144 premir rs a c CA mir-3152 mature rs a g CA mir-3152 mature rs a g mir-3166 premir rs a t IOP mir-320e premir rs a g CA mir-339 mature rs t c DA mir-339 mature rs t c IOP mir-3609 premir rs a t CA mir-3612 premir rs a g DA mir-3659 premir rs t c DA mir-3683 premir rs a t DA mir-3686 premir rs a g IOP mir-3909 premir rs a g DA mir-3928 premir rs a g mir-3936 premir rs t c DA mir-411 premir rs t c mir-4268 premir rs t c DA mir-4274 premir rs a g DA mir seed rs c g mir-4480 premir rs t g CA mir-4480 premir rs t g IOP mir-4482 premir rs t g IOP mir-4513 seed rs a g IOP mir-4532 seed rs a g DA mir-4532 seed rs a g mir-4634 premir rs a g mir-4655 mature rs t c IOP mir-4707 seed rs a c E-05 CA mir-4707 seed rs a c E-05

7 mir-4743 premir rs a g CA mir-4743 premir rs a g mir-4749 mature rs t c DA mir-4781 seed rs a g CA mir-4781 seed rs a g DA mir-4791 premir rs a g IOP mir-4792 premir rs t g IOP mir-492 premir rs c g IOP mir-499b mature rs a g CA mir-499b mature rs a g DA mir-499b mature rs a g IOP mir-520f premir rs a g CA mir-548ae-2 premir rs a g DA mir-548al seed rs a g CA mir-548al seed rs a g IOP mir-548al seed rs a g mir-548ap mature rs a g DA mir-548ap premir rs a t DA mir-548h-4 premir rs a g CA mir-548h-4 premir rs a g mir-550a-3 premir rs t c mir-550a-3 premir rs a g mir-564 premir rs c g CA mir-5680 premir rs t c CA mir-5682 premir rs a g IOP mir-5689 mature rs t c CA mir-5689 mature rs t c mir-5700 mature rs t c IOP mir-596 mature rs t c CA mir-597 premir rs a g DA mir-612 premir rs a g E-06 CA mir-612 premir rs a g E-09 mir-6130 premir rs a t DA mir-656 premir rs t c DA mir-656 premir rs t c mir-6719 premir rs a g mir p Mature rs a g DA mir p Mature rs a g DA mir premir rs t c Shown are 63 genetic variants located in 59 unique mirnas that are nominally (p < 0.05) associated with POAG endophenotypes in the publicly available IGGC GWAS data.

8 Table S6. The putative mir-612 and mir p target genes associated with and cup area mirna ID Phenotype All target genes (number of SNPs) mir (118,327) -cup areaassociated putative targets USH2A FAM101A JRK SIX4 Top SNP rs rs rs rs GWAS p-value 1.06E E E E-08 mir-612 Cup area 717 SIX4 rs E-17 (118,197) FAM101A rs E-13 mir p 1159 MYPN rs E-31 (131,887) CARD10 rs E-12 LTBP3 rs E-09 H1F0 rs E-08 FLNB rs E-08 SLC25A16 rs E-08 FRMD8 rs E-07 mir p Cup area 1159 FLNB rs E-10 (131,758) MYPN rs E-09 PFAS rs E-07 Shown are putative target genes of mir-612 and mir p associated with and cup area (using the publicly available GWAS data of POAG endophenotypes). TargetScan v7.0 (total context++ score > 0.01) and mirdb databases were used to extract the predicted target genes of the mirnas. The Bonferroni correction was used (based on the number of SNPs in the studied target genes of each mirna) to set the significance level, which is p-value < 4.2E-07 for mir-612 target genes and p-value < 3.8E-07 for mir-4707 target genes. The SNPs shown in the table are top SNPs in the mentioned target genes associated with and cup area. Bold target genes have been shown previously to be differentially expressed in the eye tissues (trabecular meshwork, aqueous humor or optic nerve) in the previous gene expression profiling studies of glaucoma patients.

9 Table S7. Expression of the putative mir-612 and mir p target genes associated with and cup area across different eye tissues Gene Probe ID USH2A FAM101A JRK SIX MYPN CARD LTBP H1F FLNB PFAS SLC25A FRMD Choroid RPE Ciliary Body Cornea Optic Nerve Retina Sclera Trabecular Meshwork Shown are expression of a number of mir-612 and mir p predicted target genes, which found to be significantly associated with and cup area, on eye tissues using the online Ocular Tissue Database. The gene expression is indicated as Affymetrix Probe Logarithmic Intensity Error (PLIER) number. The PLIER number were calculated by GC-background correction, PLIER normalization, log transformation and z-score calculation.

10 Table S8. The mirna-target gene interaction analysis using the Rotterdam Study data mirna SNP ID Target gene Top SNP Cup area (p-value) (p-value) mir-612 rs SIX4 rs USH2A rs FAM101A rs JRK rs mir-4707 rs MYPN rs CARD10 rs LTBP3 rs H1F0 rs FRMD8 rs FLNB rs SLC25A16 rs PFAS rs This table shows the interaction analysis between two identified SNPs in mir-612 and mir-4707 with the top SNP in their target genes associated with glaucoma using the Rotterdam Study (n=10,404)., the mean of vertical cup to disc ratio which is between 0 and 1 (Mean= 0.44, SD= 0.18); Cup area is between 0 and 2 (Mean= 0.54, SD= 0.34). This analysis indicates a significant interaction between mir-4707 (rs ) and CARD10 (rs ) in relation to cup area, shown in bold.

11 Table S9. Forty-seven mirna-binding site variants within the 3 UTRs of 21 genes associated with POAG endophenotypes SNP ID Gene ID Chr. Position Asso. pheno MA effect p-value GWAS A1 mirna binding sites in presence of A1 A2 mirna binding sites in presence of A2 rs CDC DA C (-) 4.00E-08 t mir p c mir-4729, mir p mir-5696, mir-579-3p mir-664b-3p rs TMCO IOP C (+) 4.23E-11 c mir-296-3p, mir-323b-5p mir-410-5p, mir-494-5p mir-511-5p t mir p, mir p mir-4675, mir-4741 mir p, mir-626 mir p rs TMCO IOP T (-) 4.35E-11 c mir-4454, mir-598-5p t mir-4299, mir-4456 mir-548q, mir-7978 rs TRIB CA T (+) 1.13E-09 t mir-545-3p, mir-583 a mir-3125, mir-3916 mir-4310, mir p mir p, mir-877-5p rs7344 SRSF CA C (+) 3.95E-07 t hsa-let-7f-2-3p, mir p mir p, mir p rs CAV IOP T(+) 1.22E-10 c mir p, mir-4435 mir p, mir-588 mir p, mir-548s c t hsa-let-7e-3p, mir p mir-548al mir-4662a-5p, mir-575 mir p, mir-6858 rs CAV IOP G (+) 1.54E-10 a mir-216b-3p g mir p rs CAV IOP G (+) 1.90E-09 g mir-224-5p, mir-377-3p t - rs PSCA A (-) 2.82E-08 a mir-1273h-3p, mir-3166 mir-342-5p, mir p mir-4771, mir p g mir p rs PSCA G (+) 2.67E-08 t mir p g mir-597-5p, mir-668-3p rs PSCA A (-) 2.50E-08 g mir p a mir-296-5p, mir p mir p rs PSCA G (-) 2.66E-08 c mir p, mir-3188 mir-3975, mir p mir-4663, mir-485-5p mir p, mir-8077, mir-7160 rs PSCA G (-) 2.38E-08 c mir-3650, mir-4455 g mir p, mir-4679 mir p, mir p mir p, mir p rs PSCA T (-) 2.53E-08 c mir-4455, mir p t mir p, mir p mir p mir p, mir p rs PSCA A (-) 2.58E-08 g mir-4537 a mir p g mir-3155a, mir-3155b mir p, mir-484

12 rs PSCA A (-) 2.49E-08 g mir-4421, mir p mir p rs ABO IOP T (+) 1.05E-08 t mir p, mir p mir-6762, mir p, mir-885-3p rs CDKN2B , CA a mir p,mir-3655 mir-4431, mir-676-3p c - G (-) 5.31E-33 a mir-382-5p g mir p, mir-323b-5p mir-410-5p mir-494-5p rs CDKN2B CA, T (+) 4.07E-18 c mir p, mir-205-3p t mir-374c-5p, mir-655-3p rs HNRNPH DA T (-) 5.77E-08 a mir-489-3p t - rs HNRNPH DA, A (-) 1.35E-24 a mir p, mir-361-5p c mir-383-5p, mir p rs MYPN DA G (+) 2.52E-15 c mir p mir-636, mir-96-5p g - rs MYPN DA C (+) 8.41E-09 c mir p, mir-624-3p g mir-133a-5p,mir-320e mir-4490 rs MYPN DA A (+) 1.20E-08 a mir-339-5p, hsa-let-7a-2-3p, g mir p hsa-let-7g-3p, mir-486-5p mir p rs MYPN DA T (+) 2.67E-15 c mir p, mir-548g-3p t mir p mir p, mir p rs PBLD DA, A (-) 3.13E-84 a mir-133a-5p, mir p g mir-138-5p, mir-7978 rs PBLD DA, A (-) 1.29E-83 a mir p, mir-1265 c mir-4493, mir p mir-605-3p, mir-6126 rs PBLD DA, T (-) 4.14E-84 t mir-3143, mir-543 c mir-141-3p, mir-200a-3p rs RUFY DA, A (-) 8.54E-20 g mir-651-3p a mir p rs RUFY DA A (-) 1.18E-07 a - g mir-32-3p, mir p mir p, mir-921 rs RUFY DA, A (-) 4.26E-25 a mir-4719 g - rs RUFY DA, G (-) 4.64E-25 a mir-6074 g mir-548ap/h, mir-559 mir-8054 rs RUFY DA, C (-) 6.82E-25 t mir p c mir-132-5p rs RUFY DA, T (-) 9.99E-25 t mir-219b-3p, mir-3123 mir-6511b-5p, mir p c mir-1205, mir-146a-5p mir-146b-5p, mir p

13 mir-4418, mir p mir-509-5p, mir p rs RUFY DA, A (-) 1.66E-24 a mir p, mir p c mir p mir-326, mir-330-5p mir-518c-5p, mir p mir p, mir p mir p, mir-767-3p rs SLC25A DA, C (-) 5.37E-19 c mir-3622b-5p, mir p t mir-564 mir p, mir p rs SLC25A DA A (-) 1.35E-15 g mir-518 a mir-4422, mir p rs CELF IOP G (+) 2.32E-07 a mir-4721 g mir-1273c rs FOLH IOP A (+) 1.29E-08 g mir-186-5p, mir-3133 mir-4509, mir-4744 a mir p, mir-548c-3p rs MAP3K C (-) 2.47E-07 c mir-124-3p, mir-1295b t mir-3910, mir-520a-5p mir-1912, mir-500b-3p, mir-506-3p mir-525-5p rs PAX DA T (+) 5.53E-08 t mir p, mir-3135b c mir-1203 mir-6081 rs1506 PAX DA T (-) 6.34E-09 a mir p, mir p t mir-500b-3p mir-370-3p, mir-4718 mir p, mir p rs PAX DA C (-) 4.21E-09 t mir-5681b, mir-5696 mir-579-3p, mir-664a-3p mir-664b-3p c mir p rs RBM A (+) 6.53E-07 g mir-3924 a mir-190a-3p, mir p mir-6083 rs AAGAB IOP C (-) 2.89E-07 t mir-329-5p, mir-4659a-3p mir-4659b-3p, mir p c mir p, mir p mir p rs PFAS CA T (-) 5.53E-07 c mir-149-3p, mir p t mir-3175, mir-3975 mir-423-5p, mir-4489 mir p, mir-8085 mir p, mir-6085 mir p, mir p mir p, mir p rs TRIOBP A (+) 3.16E-07 g mir p a mir-30a-3p, mir-30d-3p mir-30e-3p, mir p Shown are 47 glaucoma-associated variants that are predicted to affect mirna-binding sites using PolymiRTS (v3.0). DA, disc area; CA, cup area; Chr, chromosome; MA, minor allele; A1, ancestral allele; A2, alternative allele. Bold mirnas have been shown previously to be differentially expressed in the eye tissues (trabecular meshwork, aqueous humor or optic nerve) in the previous mirna expression profiling studies of glaucoma patients.

14 Table S10. Functional characteristics of 47 mirna-binding site variants associated with POAG endophenotypes SNP ID Host gene A1 A2 Chr. Position MAF Proxy SNPs Non-syn. cis-eqtl Effect allele (Europe) (R 2 > 0.8) Proxies (tissue) in eqtl (β) rs CDC7 t c Brain, Nerve, Blood, other tissues C (-) rs TMCO1 c t Nerve, Blood, Artery, other tissues C (-) rs TMCO1 c t Nerve, Blood, Artery, other tissues T (-) rs TRIB2 t a Nerve, Whole blood T (-) rs7344 SRSF3 t c Nerve, Whole blood, Skin, Thyroid C (+) rs CAV2 c t Pancreases, Testis T (-) rs CAV2 a g Pancreases, Blood G (-) rs CAV2 g t Pancreases, Blood, Lung, Testis G (-) rs PSCA a g Brain, Nerve, Blood, other tissues A (+) rs PSCA t g Brain, Nerve, Blood, other tissues G (+) rs PSCA g a Brain, Nerve, Blood, other tissues A (+) rs PSCA c g Brain, Nerve, Blood, other tissues G (+) rs PSCA c g Brain, Nerve, Blood, other tissues G (+) rs PSCA c t Brain, Nerve, Blood, other tissues T (+) rs PSCA g a Brain, Nerve, Blood, other tissues A (+) rs PSCA g a Brain, Nerve, Blood, other tissues A (+) rs ABO t c Nerve, Adipose, Heart, Lung, Skin T (+) rs CDKN2B a g Temporal cortex G (-) rs CDKN2B c t Whole blood T (+) rs MYPN c g Muscle skeletal G (+) rs MYPN c t Muscle skeletal T (+) rs MYPN c g C (+) rs MYPN a g A (+)

15 rs PBLD a g Brain, Nerve, Liver, other tissues A (+) rs PBLD a c Brain, Nerve, Liver, other tissues A (+) rs PBLD t c Brain, Nerve, Liver, other tissues T (+) rs HNRNPH3 a t T (-) rs RUFY2 a g A (-) rs RUFY2 a g Brain, Nerve, Blood, other tissues A (+) rs RUFY2 a g Brain, Nerve, Blood, other tissues G (+) rs RUFY2 t c Brain, Nerve, Blood, other tissues C (+) rs RUFY2 t c Brain, Nerve, Blood, other tissues T (+) rs RUFY2 a c Brain, Nerve, Blood, other tissues A (+) rs RUFY2 g a Brain, Nerve, Blood, other tissues A (+) rs HNRNPH3 a c Brain, Nerve, Blood, other tissues A (-) rs SLC25A16 c t Brain, Nerve, Blood, other tissues C (-) rs SLC25A16 g a Brain, Nerve, Blood, other tissues A (-) rs CELF1 a g Nerve, Muscle, Blood, other tissues G (+) rs FOLH1 g a Skin, Testis A (+) rs MAP3K11 c t Artery, Adipose, Blood, Skin C (-) rs1506 PAX6 a t T (-) rs PAX6 t c C (-) rs PAX6 t c Lymphoblastoid T (-) rs RBM23 g a Brain, Nerve, Blood, other tissues A (-) rs AAGAB t c Adipose, Lung, Skin, Thyroid C (-) rs PFAS c t Nerve, Blood, Adipose, Colon T (-) rs TRIOBP g a Nerve, Blood, Adipose, other tissues A (-) The high LD proxies and eqtl of 47 mirna-binding site SNPs associated with POAG endophenotypes using HaploReg v4.1. In total, 723 intronic and 10 missense SNPs are in LD (R 2 > 0.8) with the binding site SNPs. Bold are the most significant SNPs among the correlated SNPs in one gene.

16 Table 11. Expression of genes hosting the 47 mirna-binding site variants associated with POAG endophenotypes in eye tissues Gene ID Probe ID Trabecular Optic Choroid Ciliary Cornea Lens Retina Sclera Meshwork Nerve RPE Body AAGAB ABO CAV CDC CDKN2B CELF FOLH HNRNPH MAP3K MYPN PAX PBLD PFAS PSCA RBM RUFY SRSF SLC25A TMCO TRIB TRIOBP Expression of 21 genes hosting the 47 mirna-binding sites associated with glaucoma endophenotypes across human eye tissues (using The Ocular Tissue Database). The gene expression is indicated as Affymetrix Probe Logarithmic Intensity Error (PLIER) number. The PLIER number were calculated by GC-background correction, PLIER normalization, log transformation and z-score calculation.

17 Table S12. Prioritization of 47 mirna-binding site variants associated with glaucoma endophenotypes SNP ID Top in GWAS eqtl MA (effect) Proxy SNPs (# non-syn) Gene ID Gene exp in the eye Gene asso with dis MiRNA-binding site (disruption/creation) mir exp in the eye mir asso with dis rs T (+) 4 (0) CDKN2B mir p 9 rs G (-) 29 (0) CDKN2B mir-323-5p 8 rs G (-) 11 (0) CAV2 mir-224-5p 8 rs C (-) 74 (0) AAGAB mir-329-5p - 8 rs A (+) 48 (0) PSCA mir-342-5p, mir p - 8 rs T (-) 5 (0) PFAS mir-149-3p, mir-423-5p - 8 rs T (-) 10 (0) TRIB2 mir-877-5p - 8 rs A (-) 1 (0) RBM23 mir-190a-3p - 8 rs T (+) 7 (1) ABO mir-885-3p - 8 rs7344 C (+) 64 (0) SFRS3 mir-548al, Let-7f-2-3p - 8 rs G (+) 48 (0) PSCA mir-597-5p - 8 rs G (+) 81 (0) RUFY2 mir-548ap/h, mir rs A (+) 81 (0) RUFY2 mir p - 7 rs C (+) 81 (0) RUFY2 mir-132-5p - 7 rs A (+) 81 (0) RUFY2 mir p - 7 rs T (+) 81 (0) RUFY2 mir-219b-3p - 7 rs T (-) 10 (1) CAV2 mir p, mir rs C (-) 33 (0) TMCO1 mir-323-5p, mir-410-5p - 7 rs G (+) 48 (0) PSCA mir-485-5p - 7 rs G (+) 11 (0) MYPN mir p, mir-96-5p - 6 rs A (+) 48 (0) PSCA mir-676-3p - 6 rs A (+) 30 (1) PBLD mir p rs T (+) 11 (0) MYPN mir-548g-3p - 6 rs A (+) 48 (0) PSCA mir-296-5p - 6 rs G (-) 10 (1) CAV2 mir p - 6 rs C (-) 15 (0) CDC7 mir-579-3p rs C (+) 22 (0) MYPN mir-320e, mir-133a - 6 Score

18 rs G (+) 30 (0) CELF1 mir-1273c rs C (-) 4 (0) PAX6 mir-664a-3p - 5 rs T (-) 4 (0) PAX6 mir-370-3p - 5 rs G (+) 48 (0) PSCA mir p rs C (-) 20 (0) MAP3K11 mir-520a, mir rs T (-) 33 (0) TMCO1 mir-548q - 5 rs T (+) 30 (1) PBLD mir rs A (+) 60 (2) FOLH1 mir-186-5p - 5 rs A (-) 61 (2) TRIOBP mir-30a-3p - 5 rs A (+) 30 (1) PBLD mir-133a-5p - 5 rs A (+) 81 (0) RUFY2 mir rs T (-) 3 (0) PAX6 mir-3135b rs C (-) 26 (0) SLC25A16 mir rs A (+) 22 (0) MYPN mir-339-5p, Let-7a-2-3p - 5 rs A (-) 81 (0) HNRNPH3 mir-361-5p - 4 rs A (-) 60 (0) SLC25A16 mir rs A (+) 48 (0) PSCA mir p rs T (+) 48 (0) PSCA mir p rs A (-) 30 (1) RUFY2 mir-32-3p - 3 rs T (-) 30 (1) HNRNPH3 mir-489-3p - 3 Prioritization of the 47 mirna-binding site SNPs associated with POAG endophenotypes. A functional score (between 1 and 10) was calculated for each SNP by combining the results of our predefined criteria including the strength of association, LD pattern, eqtl data, expression and importance of the related mirna and target gene in the eye. 1. The strength of the association in GWAS results: Lead SNP (2), One of the top 10% SNPs in the locus (1), Only passed the threshold (0). 2. The eqtl data: Correlation between SNP and expression of the host gene (2), Correlation of SNPs with expression of the nearby genes in the locus (1), No correlation (0). 3. The LD pattern: No or just a few synonymous proxies (2), Several synonymous proxies, but no non-synonymous (1), Several proxies including nonsynonymous proxy SNPs (0). 4. Host gene: Expressed in the eye and previously reported to be involved in POAG (2), Expressed in the eye or involved in POAG (1), Not expressed in the eye and no evidence to be involved in POAG (0). 5. mirna: Expressed in the eye and previously reported to be involved in the eye disease (2), Expressed in the eye or involved in the eye disease (1), Not expressed in the eye and no evidence to be involved in the eye disease (0). One extra point for the mirna-target interactions that are validated.

19 Figure S1. The predicted hairpin structure of pre-mir-612 and pre-mir-4707 and the position of two identified variants associated with and cup area pre-mir ca --a c cu c - -a a 5' ucc ucugg cc ug ggg agggcuucug agcuccuu gc c 3' agg ggacc gg ac ccc ucccggggac ucggggag cg u acucuc aca gac u cu - c ga a rs (G/A) pre-mir-4707 u - c gc -- ug - u 5' ggu ccg gagcc cggc gggcggguu c g ggug a 3' cca ggc cuugg gccg cccgcccga g c ucgc g c u a ac cc gu g a rs (T/G)

20 Figure S2. Manhattan plots showing the association of 72,052 mirna-binding site variants with POAG endophenotypes

21

22 Figure S3. Regional plots showing the association of ten highlighted mirna-binding site variants with POAG endophenotypes

23