Table 2 GWAS-eQTL Co-localized Loci
Chr GWAS Locus Start GWAS Locus End GWAS Lead SNP GWAS p Value eSNP eSNP p Value Primary/Conditional PPH4 Gene Relevant Tissue/Cell Type/Developmental Period
1 2372401 2402501 rs4648845 4.03E−09 rs12037821 4.9E−04 conditional 0.87 SLC35E2 –/–/early mid-prenatal
1 8355697 8638984 rs301797 2.03E−09 rs138050288 1.8E−04 primary 0.95 RERE –/–/–
1 30412551 30443951 rs1498232 1.28E−09 rs2015244 1.8E−08 primary 0.99 PTPRU –/neurons /early mid-prenatal
1 163582923 163766623 rs7521492 5.64E−07 rs10799961 3.18E−11 primary 0.91 PBX1 –/–/early prenatal
1 205015255 205189455 rs16937 8.69E−07 rs12724651 7.31E−07 primary 0.89 TMEM81 –/neurons/–
rs12031350 8.15E−06 conditional 0.87 RBBP5 –/–/–
1 214137889 214163689 rs7529073 9.69E−07 rs1431983 1.67E−04 conditional 0.93 PROX1-AS1 cerebellar hemisphere/neurons/adult
2 73194203 73900439 rs56145559 8.42E−08 rs11679809 1.85E−34 primary 0.86 ALMS1P testis/–/–
2 110262036 110398236 rs9330316 7.69E−08 rs892464 2.35E−26 primary 0.92 SEPT10 –/–/late prenatal
2 198148577 198835577 rs6434928 1.48E−11 rs12621129 6.06E−12 primary 0.94 SF3B1 –/–/–
2 200715237 201247789 rs281768 1.78E−14 rs35220450 3.46E−14 primary 0.95 FTCDNL1, AC073043.2 –/–/adult
rs186546506 8.77E−04 conditional 0.83 LINC01792, AC007163.3 putamen (basal ganglia)/ –/adult
2 208371631 208531731 rs2709410 5.75E−07 rs34171849 5.86E−17 primary 0.88 METTL21A –/–/–
rs2551656 2.85E−09 primary 0.86 CREB1 –/–/early prenatal
2 220033801 220071601 rs6707588 9.51E−07 rs13404754 1.08E−09 primary 0.92 CNPPD1 –/–/–
3 36843183 36945783 rs75968099 3.39E−12 rs9834970 1.88E−05 primary 0.94 DCLK3 nerve - tibial /neurons/infant
3 52281078 53539269 rs2535627 3.96E−11 rs6801235 2.81E−08 conditional 0.86 PPM1M –/neurons/late prenatal
3 63792650 64004050 rs832187 2.58E−08 rs113386200 1.95E−12 primary 0.98 THOC7 –/–/–
3 135807405 136615405 rs7432375 5.27E−11 rs10935184 7.71E−25 primary 0.93 PCCB –/–/–
4 170357552 170646052 rs10520163 1.02E−08 rs7438 1.02E−09 primary 0.97 CLCN3 –/–/–
5 45291475 46404116 rs1501357 1.24E−08 rs9292918 4.45E−05 primary 0.94 BRCAT54, RP11-53O19.1 –/–/adult
6 83779798 84407274 rs3798869 8.57E−10 rs2016358 1.19E−09 primary 0.90 SNAP91 cerebellar hemisphere/–/–
6 108875527 109019327 rs9398171 3.37E−08 rs111727905 3.84E−06 primary 0.97 ZNF259P1 –/–/early mid-prenatal
7 21485312 21545712 rs73060317 6.60E−07 rs141984481 3.59E−05 primary 0.92 SP4 –/–/early prenatal
8 8088038 10056127 rs2945232 2.03E−08 rs2980441 7.68E−69 primary 0.82 FAM86B3P –/–/adolescent
8 26181524 26279124 rs1042992 2.27E−07 rs17055186 3.06E−24 conditional 0.91 SDAD1P1 testis/–/adult
8 38020424 38310924 rs57709857 2.32E−07 rs201999919 1.70E−07 primary 0.88 WHSC1L1 –/–/early prenatal
8 144822546 144871746 rs11784536 1.83E−07 rs12541792 6.45E−35 primary 0.90 FAM83H esophagus - mucosa/oligodendrocytes/adolescent
9 26839508 26909408 rs10967586 4.75E−07 rs12345197 3.90E−06 primary 0.80 IFT74 –/–/–
11 46340213 46751213 rs7951870 1.97E−11 rs16938506 5.08E−05 primary 0.88 MDK –/–/early mid-prenatal
12 57428314 57497814 rs324017 2.13E−07 rs4559 2.02E−05 conditional 0.91 STAT6 –/microglia/adolescent
14 35421614 35847614 rs77477310 1.52E−07 rs1028449 8.09E−04 primary 0.84 RP11-85K15.2 –/–/–
15 78803032 78926732 rs8042374 1.87E−12 rs7171869 1.44E−04 conditional 0.94 IREB2 –/–/early prenatal
15 84661161 85153461 rs950169 7.62E−11 rs35677834 1.54E−34 primary 0.80 LOC101929479, RP11-561C5.3 ovary/–/early mid-prenatal
15 91416560 91436560 rs4702 2.30E−12 rs4702 4.49E−13 primary 1.00 FURIN –/endothelial cells/adolescent
16 4447751 4596451 rs6500602 2.79E−07 rs3747580 4.75E−16 primary 0.90 CORO7 –/–/–
rs8046295 2.68E−11 primary 0.89 NMRAL1 –/–/–
16 29924377 30144877 rs12691307 1.30E−10 rs4788203 1.95E−05 primary 0.88 TMEM219 –/–/–
rs3935873 7.46E−14 primary 0.87 INO80E –/neurons/–
rs4787491 1.60E−04 conditional 0.82 DOC2A brain - cortex/neurons/adolescent
16 58669293 58691393 rs12325245 1.15E−08 rs11647976 4.83E−04 primary 0.94 CNOT1 –/–/–
17 17722402 18030202 rs8082590 6.84E−09 rs4072739 4.74E−13 primary 0.92 DRG2 –/–/–
19 11839736 11859736 rs72986630 4.64E−08 rs72986630 2.20E−14 primary 1.00 ZNF823 –/endothelial cells/early prenatal
19 19374022 19658022 rs2905426 6.92E−09 rs2965199 9.22E−36 primary 0.87 GATAD2A –/–/–
19 50067499 50135399 rs56873913 2.19E−07 rs5023763 9.32E−05 primary 0.93 SNRNP70 –/–/–
22 41408556 42689414 rs9607782 6.76E−12 rs200447424 1.87E−04 primary 0.96 RANGAP1 –/–/–