Supplemental Table 1: Results (P-Values) of Gene-Based Analyses of Genes

Supplemental Table 1: Results (p-values) of gene-based analyses of genes

in the vascular tone pathway using data from the combined GLAUGEN and NEIGHBOR

for the association with primary open-angle glaucoma

Gene / Chr / N Simple Features* / N Complex Features* / Gene p value†,
AGT / 1 / 7 / 10 / 0.60
AKT3 / 1 / 5 / 5 / 0.26
AQP10 / 1 / 3 / 6 / >0.99
AVPR1B / 1 / 9 / 0 / >0.99
CHRM3 / 1 / 17 / 23 / 0.91
CLCNKB / 1 / 4 / 5 / >0.99
CYP4A11 / 1 / 0 / 2 / >0.99
ECE1 / 1 / 14 / 9 / >0.99
GNAI3 / 1 / 3 / 6 / 0.01
GNB1 / 1 / 0 / 2 / >0.99
GNG4 / 1 / 9 / 8 / 0.17
MTHFR / 1 / 3 / 6 / 0.27
NPPA / 1 / 1 / 6 / >0.99
PIK3C2B / 1 / 10 / 4 / >0.99
PIK3CD / 1 / 4 / 4 / 0.02
PIK3R3 / 1 / 1 / 2 / >0.99
PRKAA2 / 1 / 8 / 8 / 0.01
PRKAB2 / 1 / 0 / 2 / >0.99
PRKACB / 1 / 7 / 6 / 0.44
PTGS2 / 1 / 0 / 3 / 0.09
REN / 1 / 6 / 7 / 0.14
S1PR1 / 1 / 4 / 6 / >0.99
SDHB / 1 / 8 / 8 / >0.99
SDHC / 1 / 6 / 3 / >0.99
ADCY3 / 2 / 3 / 7 / 0.44
AQP12A / 2 / 10 / 5 / >0.99
AQP12B / 2 / 5 / 4 / 0.20
CALM2 / 2 / 4 / 6 / >0.99
CUL3 / 2 / 1 / 5 / 0.24
PDE1A / 2 / 4 / 11 / 0.18
PRKAG3 / 2 / 3 / 4 / 0.18
PRKCE / 2 / 89 / 39 / 0.12
PRKD3 / 2 / 5 / 4 / 0.23
ADCY5 / 3 / 4 / 8 / 0.16
AGTR1 / 3 / 31 / 8 / 0.01
GNAI2 / 3 / 4 / 2 / 0.004
GNB4 / 3 / 0 / 6 / >0.99
ITPR1 / 3 / 62 / 31 / 0.33
KNG1 / 3 / 9 / 11 / 0.58
MECOM / 3 / 5 / 6 / 0.28
MYLK / 3 / 8 / 6 / >0.99
PIK3CA / 3 / 9 / 1 / >0.99
PIK3CB / 3 / 2 / 2 / >0.99
PIK3R4 / 3 / 2 / 3 / 0.14
PRKAR2A / 3 / 0 / 1 / >0.99
PRKCD / 3 / 5 / 6 / 0.002
SLC4A7 / 3 / 4 / 4 / 0.04
ULK4 / 3 / 13 / 14 / >0.99
VHL / 3 / 7 / 4 / >0.99
EDNRA / 4 / 7 / 7 / 0.14
FGF5 / 4 / 10 / 3 / 0.06
GUCY1A3 / 4 / 14 / 8 / >0.99
GUCY1B3 / 4 / 6 / 8 / >0.99
KDR / 4 / 4 / 6 / 0.38
NR3C2 / 4 / 15 / 18 / 0.04
PDE5A / 4 / 2 / 3 / 0.10
PDE6B / 4 / 6 / 1 / >0.99
ADCY2 / 5 / 27 / 24 / >0.99
ADRA1B / 5 / 5 / 6 / 0.39
ADRB2 / 5 / 10 / 6 / 0.05
KLHL3 / 5 / 4 / 5 / >0.99
NPR3 / 5 / 10 / 8 / >0.99
PDE6A / 5 / 11 / 11 / 0.04
PIK3R1 / 5 / 8 / 9 / 0.07
PRKAA1 / 5 / 0 / 2 / < 0.001
SDHA / 5 / 2 / 4 / 0.001
EDN1 / 6 / 5 / 6 / 0.30
ESR1 / 6 / 22 / 20 / 0.02
HFE / 6 / 0 / 2 / < 0.001
ITPR3 / 6 / 14 / 9 / < 0.001
VEGFA / 6 / 12 / 9 / 0.24
AQP1 / 7 / 13 / 8 / >0.99
CAV1 / 7 / 2 / 6 / < 0.001
GNAI1 / 7 / 7 / 9 / 0.26
GNB2 / 7 / 0 / 2 / < 0.001
MYL10 / 7 / 2 / 6 / 0.06
NOS3 / 7 / 4 / 4 / 0.05
PDE1C / 7 / 33 / 22 / 0.71
PIK3CG / 7 / 8 / 5 / 0.13
PRKAG2 / 7 / 48 / 25 / 0.04
PRKAR1B / 7 / 0 / 1 / >0.99
PRKAR2B / 7 / 1 / 6 / >0.99
TBXAS1 / 7 / 29 / 18 / 0.01
ADCY8 / 8 / 18 / 16 / 0.78
ADRA1A / 8 / 22 / 16 / 0.90
CYP11B1 / 8 / 1 / 2 / >0.99
AQP3 / 9 / 6 / 7 / 0.34
AQP7 / 9 / 7 / 5 / >0.99
PRKACG / 9 / 7 / 6 / >0.99
PTGS1 / 9 / 5 / 6 / >0.99
S1PR3 / 9 / 2 / 8 / 0.34
ADRB1 / 10 / 11 / 3 / 0.07
CACNB2 / 10 / 55 / 27 / 0.62
CYP17A1 / 10 / 0 / 5 / >0.99
PDE6C / 10 / 13 / 7 / >0.99
PRKCQ / 10 / 18 / 12 / 0.33
PRKG1 / 10 / 94 / 56 / 0.98
RET / 10 / 4 / 4 / >0.99
AQP11 / 11 / 0 / 2 / >0.99
GNG3 / 11 / 1 / 1 / >0.99
GUCY1A2 / 11 / 18 / 20 / 0.05
KCNJ1 / 11 / 9 / 9 / 0.48
LSP1 / 11 / 11 / 5 / 0.31
PDE2A / 11 / 13 / 11 / 0.64
PIK3C2A / 11 / 0 / 1 / >0.99
PLCB3 / 11 / 0 / 4 / >0.99
SDHAF2 / 11 / 1 / 2 / >0.99
SDHD / 11 / 2 / 2 / >0.99
SOX6 / 11 / 13 / 6 / >0.99
TNNT3 / 11 / 6 / 6 / >0.99
AQP5 / 12 / 8 / 5 / 0.30
ATP2B1 / 12 / 3 / 3 / 0.14
AVPR1A / 12 / 1 / 4 / >0.99
GNB3 / 12 / 6 / 6 / >0.99
ITPR2 / 12 / 36 / 28 / 0.03
PDE1B / 12 / 3 / 12 / 0.42
PDE6H / 12 / 4 / 5 / 0.08
PIK3C2G / 12 / 16 / 17 / 0.85
PRKAB1 / 12 / 1 / 3 / >0.99
PRKAG1 / 12 / 1 / 2 / 0.08
SH2B3 / 12 / 0 / 2 / 0.05
TBX3 / 12 / 6 / 7 / >0.99
TBX5 / 12 / 6 / 11 / 0.002
WNK1 / 12 / 0 / 2 / >0.99
EDNRB / 13 / 0 / 1 / < 0.001
FLT1 / 13 / 9 / 11 / >0.99
GUCY1B2 / 13 / 7 / 11 / 0.02
SLC7A1 / 13 / 17 / 6 / >0.99
ADCY4 / 14 / 7 / 5 / >0.99
AKT1 / 14 / 3 / 2 / 0.04
BDKRB2 / 14 / 19 / 14 / >0.99
CALM1 / 14 / 6 / 4 / 0.26
ESR2 / 14 / 2 / 7 / 0.35
GNG2 / 14 / 26 / 14 / 0.38
HSP90AA1 / 14 / 3 / 4 / >0.99
PRKCH / 14 / 31 / 18 / >0.99
PRKD1 / 14 / 15 / 10 / >0.99
AQP9 / 15 / 11 / 8 / >0.99
CSK / 15 / 2 / 3 / 0.21
GNB5 / 15 / 5 / 4 / >0.99
PLCB2 / 15 / 17 / 4 / 0.40
SLC12A1 / 15 / 2 / 2 / >0.99
ADCY7 / 16 / 6 / 5 / 0.05
ADCY9 / 16 / 21 / 16 / 0.83
AQP8 / 16 / 4 / 5 / 0.05
HSD11B2 / 16 / 0 / 2 / >0.99
PLCG2 / 16 / 51 / 19 / 0.53
PDPK1 / 16 / 0 / 0 / >0.99
PRKCB / 16 / 29 / 20 / 0.10
SCNN1B / 16 / 13 / 5 / 0.39
SCNN1G / 16 / 6 / 2 / >0.99
SLC12A3 / 16 / 13 / 6 / 0.08
UMOD / 16 / 10 / 6 / 0.34
ACE / 17 / 5 / 4 / >0.99
PDE6G / 17 / 5 / 2 / >0.99
PIK3R5 / 17 / 10 / 8 / >0.99
PLCD3 / 17 / 6 / 5 / 0.01
PRKAR1A / 17 / 1 / 6 / >0.99
PRKCA / 17 / 32 / 26 / 0.03
WNK4 / 17 / 4 / 1 / >0.99
ZNF652 / 17 / 7 / 5 / >0.99
AQP4 / 18 / 7 / 10 / 0.07
MYL12B / 18 / 5 / 5 / 0.27
PIK3C3 / 18 / 0 / 3 / >0.99
AKT2 / 19 / 0 / 3 / >0.99
CALM3 / 19 / 13 / 3 / >0.99
CYP4F2 / 19 / 2 / 8 / >0.99
DNM2 / 19 / 2 / 7 / < 0.001
PIK3R2 / 19 / 2 / 4 / >0.99
PRKACA / 19 / 2 / 1 / >0.99
PRKCG / 19 / 8 / 3 / 0.14
PTGIR / 19 / 9 / 4 / 0.23
S1PR2 / 19 / 3 / 4 / >0.99
S1PR4 / 19 / 4 / 6 / >0.99
S1PR5 / 19 / 6 / 4 / 0.01
ADRA1D / 20 / 13 / 6 / >0.99
AVP / 20 / 14 / 6 / >0.99
EDN3 / 20 / 6 / 7 / >0.99
GNAS / 20 / 7 / 9 / >0.99
MYL9 / 20 / 0 / 1 / < 0.001
PLCB1 / 20 / 60 / 43 / 0.83
PLCB4 / 20 / 22 / 17 / 0.89
PLCG1 / 20 / 1 / 2 / 0.003
PTGIS / 20 / 14 / 7 / 0.45
PDE9A / 21 / 19 / 12 / 0.75
ADORA2A / 22 / 0 / 1 / >0.99

Abbreviations: GLAUGEN=the Glaucoma Genes and Environment study; NEIGHBOR =National Eye Institute Glaucoma Human Genetics Collaboration ; Chr=chromosome

* Simple features refer to single SNPs not in any LD block; complex features refer to LD blocks with 2 or more SNPs.

† P-values are permuted p-values. P-values <0.05 are in bold.

Supplementary Table 2. Odds ratios (95% Confidence Interval) and p-values for SNPs in genes associated with

overall primary open-angle glaucoma (POAG) in genes-based analyses.

Gene / Chr / SNP / Gene
Location / Minor
Allele / GLAUGEN / NEIGHBOR / POOLED
Odds Ratio of POAG
per minor allele
(95% Confidence Interval) / p-value / Odds Ratio of POAG
per minor allele
(95% Confidence Interval) / p-value / Odds Ratio of POAG
per minor allele
(95% Confidence Interval) / p-value / p-value for
heterogeneity
PRKAA1 / 5 / rs1001684 / flanking_5UTR / A / 1.08(0.93,1.27) / 0.32 / 1.04(0.93,1.16) / 0.51 / 1.05(0.96,1.16) / 0.27 / NS
PRKAA1 / 5 / rs10065570 / flanking_5UTR / A / 1.09(0.94,1.27) / 0.26 / 1.05(0.94,1.17) / 0.39 / 1.06(0.97,1.16) / 0.18 / NS
PRKAA1 / 5 / rs10074991 / intron / A / 1.05(0.90,1.22) / 0.56 / 1.07(0.96,1.19) / 0.22 / 1.06(0.97,1.16) / 0.19 / NS
PRKAA1 / 5 / rs10512747 / coding / A / 0.89(0.72,1.10) / 0.28 / 0.96(0.82,1.12) / 0.59 / 0.93(0.82,1.06) / 0.29 / NS
PRKAA1 / 5 / rs1070444 / flanking_5UTR / A / 0.82(0.67,1.01) / 0.06 / 0.89(0.78,1.02) / 0.09 / 0.87(0.77,0.97) / 0.02 / NS
PRKAA1 / 5 / rs10737963 / 3UTR / C / 0.90(0.76,1.05) / 0.18 / 0.97(0.87,1.08) / 0.58 / 1.06(0.97,1.16) / 0.22 / NS
PRKAA1 / 5 / rs10941525 / intron / A / 1.00(0.87,1.15) / 0.98 / 0.96(0.87,1.06) / 0.42 / 0.97(0.90,1.06) / 0.53 / NS
PRKAA1 / 5 / rs11747210 / intron / C / 1.02(0.89,1.18) / 0.77 / 0.95(0.86,1.05) / 0.32 / 1.03(0.95,1.12) / 0.53 / NS
PRKAA1 / 5 / rs11749180 / intron / A / 0.87(0.72,1.06) / 0.16 / 0.91(0.79,1.04) / 0.15 / 0.89(0.80,1.00) / 0.05 / NS
PRKAA1 / 5 / rs12173270 / flanking_3UTR / G / 1.24(0.78,1.95) / 0.36 / 1.34(0.99,1.81) / 0.06 / 0.76(0.59,0.99) / 0.04 / NS
PRKAA1 / 5 / rs12188129 / intron / A / 0.90(0.74,1.09) / 0.27 / 0.89(0.78,1.02) / 0.09 / 0.89(0.80,1.00) / 0.05 / NS
PRKAA1 / 5 / rs17239241 / intron / G / 0.85(0.66,1.09) / 0.20 / 1.00(0.84,1.19) / 0.98 / 1.06(0.92,1.22) / 0.45 / NS
PRKAA1 / 5 / rs173969 / intron / A / 1.00(0.87,1.16) / 0.96 / 1.02(0.92,1.13) / 0.71 / 1.01(0.93,1.10) / 0.75 / NS
PRKAA1 / 5 / rs2291782 / 3UTR / A / 1.11(0.96,1.30) / 0.16 / 1.00(0.90,1.12) / 0.93 / 1.04(0.95,1.14) / 0.37 / NS
PRKAA1 / 5 / rs249414 / intron / A / 0.95(0.81,1.10) / 0.46 / 1.00(0.90,1.11) / 0.94 / 0.98(0.90,1.07) / 0.72 / NS
PRKAA1 / 5 / rs257009 / intron / G / 0.94(0.80,1.09) / 0.40 / 0.99(0.89,1.10) / 0.83 / 1.03(0.94,1.13) / 0.51 / NS
PRKAA1 / 5 / rs3792826 / intron / A / 1.10(0.83,1.45) / 0.52 / 1.04(0.85,1.26) / 0.73 / 1.06(0.90,1.25) / 0.52 / NS
PRKAA1 / 5 / rs3805486 / intron / G / 1.01(0.83,1.24) / 0.90 / 1.08(0.94,1.24) / 0.29 / 0.95(0.84,1.06) / 0.36 / NS
PRKAA1 / 5 / rs3805492 / intron / G / 1.12(0.95,1.31) / 0.17 / 1.02(0.91,1.14) / 0.72 / 0.95(0.87,1.04) / 0.28 / NS
PRKAA1 / 5 / rs4345353 / intron / G / 0.89(0.76,1.05) / 0.16 / 0.97(0.87,1.08) / 0.59 / 1.06(0.97,1.16) / 0.22 / NS
PRKAA1 / 5 / rs4546432 / intron / G / 0.99(0.86,1.14) / 0.91 / 1.01(0.91,1.12) / 0.82 / 1.00(0.92,1.08) / 0.91 / NS
PRKAA1 / 5 / rs461404 / flanking_5UTR / G / 0.94(0.81,1.10) / 0.43 / 0.99(0.89,1.10) / 0.88 / 1.03(0.94,1.12) / 0.57 / NS
PRKAA1 / 5 / rs6868112 / flanking_3UTR / C / 1.03(0.90,1.19) / 0.67 / 0.95(0.86,1.05) / 0.31 / 1.02(0.94,1.11) / 0.58 / NS
PRKAA1 / 5 / rs6882903 / intron / A / 0.91(0.78,1.07) / 0.25 / 0.94(0.85,1.05) / 0.30 / 0.93(0.85,1.02) / 0.14 / NS
PRKAA1 / 5 / rs7725810 / flanking_3UTR / G / 1.02(0.88,1.17) / 0.81 / 0.94(0.86,1.04) / 0.26 / 1.03(0.95,1.12) / 0.45 / NS
HFE / 6 / rs10484432 / flanking_3UTR / A / 1.13(0.96,1.34) / 0.15 / 1.07(0.95,1.21) / 0.25 / 1.09(0.99,1.21) / 0.08 / NS
HFE / 6 / rs10484434 / flanking_3UTR / A / 0.99(0.81,1.20) / 0.91 / 1.01(0.88,1.17) / 0.84 / 1.01(0.89,1.13) / 0.93 / NS
HFE / 6 / rs12216125 / flanking_3UTR / A / 1.23(1.06,1.42) / 0.01 / 1.04(0.93,1.15) / 0.51 / 1.10(1.01,1.20) / 0.03 / NS
HFE / 6 / rs129128 / flanking_3UTR / G / 1.25(1.03,1.53) / 0.03 / 1.01(0.87,1.17) / 0.89 / 0.92(0.81,1.03) / 0.15 / NS
HFE / 6 / rs1540275 / flanking_5UTR / A / 0.92(0.79,1.07) / 0.27 / 0.94(0.85,1.04) / 0.22 / 0.93(0.86,1.02) / 0.11 / NS
HFE / 6 / rs1543680 / flanking_5UTR / A / 1.16(0.98,1.38) / 0.08 / 1.09(0.96,1.23) / 0.18 / 1.11(1.01,1.23) / 0.04 / NS
HFE / 6 / rs1572982 / intron / A / 0.97(0.84,1.11) / 0.62 / 1.01(0.92,1.12) / 0.81 / 1.00(0.92,1.08) / 0.92 / NS
HFE / 6 / rs16891235 / coding / G / 0.89(0.71,1.12) / 0.33 / 1.02(0.87,1.20) / 0.77 / 1.02(0.89,1.17) / 0.75 / NS
HFE / 6 / rs16891315 / flanking_5UTR / G / 0.85(0.68,1.07) / 0.16 / 1.02(0.87,1.19) / 0.84 / 1.04(0.92,1.19) / 0.52 / NS
HFE / 6 / rs16891334 / flanking_5UTR / G / 0.86(0.68,1.08) / 0.19 / 1.03(0.88,1.21) / 0.70 / 1.03(0.90,1.18) / 0.66 / NS
HFE / 6 / rs17531978 / flanking_3UTR / G / 0.93(0.76,1.13) / 0.44 / 0.96(0.84,1.11) / 0.60 / 1.05(0.94,1.18) / 0.38 / NS
HFE / 6 / rs17596719 / flanking_3UTR / A / 0.95(0.77,1.16) / 0.60 / 0.98(0.85,1.14) / 0.80 / 0.97(0.86,1.09) / 0.61 / NS
HFE / 6 / rs1800562 / coding / A / 1.06(0.79,1.42) / 0.69 / 1.06(0.86,1.30) / 0.59 / 1.06(0.89,1.25) / 0.51 / NS
HFE / 6 / rs198806 / flanking_3UTR / A / 1.00(0.87,1.15) / >0.99 / 1.01(0.91,1.11) / 0.88 / 1.01(0.93,1.09) / 0.90 / NS
HFE / 6 / rs198828 / flanking_3UTR / G / 1.01(0.88,1.15) / 0.94 / 1.01(0.91,1.11) / 0.90 / 0.99(0.92,1.08) / 0.88 / NS
HFE / 6 / rs198834 / flanking_5UTR / A / 0.94(0.82,1.09) / 0.44 / 0.95(0.86,1.05) / 0.32 / 0.95(0.87,1.03) / 0.21 / NS
HFE / 6 / rs198838 / flanking_5UTR / A / 0.96(0.84,1.10) / 0.59 / 1.01(0.91,1.11) / 0.87 / 0.99(0.92,1.08) / 0.86 / NS
HFE / 6 / rs198845 / coding / A / 0.94(0.82,1.09) / 0.41 / 0.96(0.86,1.06) / 0.37 / 0.95(0.88,1.03) / 0.23 / NS
HFE / 6 / rs198853 / flanking_5UTR / G / 0.93(0.80,1.08) / 0.33 / 0.93(0.84,1.03) / 0.17 / 1.08(0.99,1.17) / 0.10 / NS
HFE / 6 / rs199750 / flanking_3UTR / G / 0.94(0.81,1.09) / 0.39 / 0.95(0.85,1.05) / 0.29 / 1.06(0.97,1.16) / 0.18 / NS
HFE / 6 / rs2009610 / coding / A / 1.18(1.00,1.39) / 0.05 / 1.06(0.94,1.19) / 0.35 / 1.10(1.00,1.21) / 0.06 / NS
HFE / 6 / rs2013063 / flanking_3UTR / A / 1.15(1.00,1.32) / 0.05 / 1.04(0.94,1.14) / 0.49 / 1.07(0.99,1.16) / 0.10 / NS
HFE / 6 / rs2032447 / flanking_5UTR / A / 0.92(0.80,1.07) / 0.27 / 0.95(0.86,1.06) / 0.35 / 0.94(0.87,1.03) / 0.17 / NS
HFE / 6 / rs2051538 / flanking_3UTR / A / 0.99(0.82,1.20) / 0.95 / 1.02(0.89,1.17) / 0.80 / 1.01(0.90,1.13) / 0.87 / NS
HFE / 6 / rs2051542 / coding / A / 1.00(0.75,1.32) / 0.99 / 1.00(0.83,1.21) / 0.99 / 1.00(0.85,1.17) / >0.99 / NS
HFE / 6 / rs2213284 / 3UTR / G / 0.89(0.77,1.04) / 0.14 / 0.93(0.84,1.03) / 0.18 / 1.09(1.00,1.19) / 0.05 / NS
HFE / 6 / rs2230655 / coding / G / 0.92(0.80,1.07) / 0.30 / 0.94(0.85,1.04) / 0.25 / 1.07(0.98,1.16) / 0.13 / NS
HFE / 6 / rs2237231 / flanking_3UTR / A / 0.88(0.68,1.15) / 0.35 / 0.99(0.83,1.19) / 0.92 / 0.95(0.82,1.11) / 0.54 / NS
HFE / 6 / rs2794719 / intron / C / 1.15(1.00,1.32) / 0.05 / 1.03(0.93,1.13) / 0.62 / 0.94(0.86,1.02) / 0.13 / NS
6 / rs2856646 / flanking_3UTR / A / 1.08(0.93,1.26) / 0.29 / 0.98(0.88,1.10) / 0.75 / 1.02(0.93,1.11) / 0.71 / NS
HFE / 6 / rs6918586 / flanking_3UTR / G / 0.98(0.86,1.13) / 0.79 / 1.04(0.94,1.15) / 0.48 / 0.98(0.91,1.07) / 0.69 / NS
HFE / 6 / rs707889 / intron / A / 1.17(0.98,1.38) / 0.07 / 1.08(0.95,1.21) / 0.23 / 1.11(1.00,1.22) / 0.05 / NS
HFE / 6 / rs707896 / flanking_3UTR / A / 1.19(0.98,1.44) / 0.07 / 1.07(0.94,1.23) / 0.31 / 1.11(0.99,1.24) / 0.06 / NS
HFE / 6 / rs707899 / flanking_3UTR / A / 1.11(0.92,1.35) / 0.27 / 1.09(0.95,1.25) / 0.23 / 1.10(0.98,1.23) / 0.11 / NS