Table 4.
Summary of eQTL in brain from Braineac and GTEx
| eQTL | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| Braineac | GTEx | ||||||||||||
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| SNP | bp | Risk allele | Chr | Location | Nearest gene | Gene | Brain region | p-value | Effect of risk allele |
Gene | Brain region | p-value | Effect of risk allele |
| rs7664889 | 77087704 | / | 4 | Intronic | SCARB2 | no eQTL | no eQTL | ||||||
| rs9268877 | 32431147 | A | 6 | Intergenic | HLA-DRA | HLA-DPA1 | Frontal cortex | 3.1×10−5 | increased expression |
HLA-DRB1 HLA-DQA2 |
Cerebellum Anterior cingulate cortex Putamen Cerebellum |
5.2×10−8
8.8×10−8 8.9×10−7 1.3×10−6 |
Increased expression Decreased expression |
| rs676768 | 116030773 | / | 10 | Intronic | VWA2 | no eQTL | no eQTL | ||||||
| rs10784359 | 40445750 | / | 12 | Intronic | SLC2A13 | no eQTL | no eQTL | ||||||
| rs2893253 | 107067203 | / | 13 | Intergenic | EFNB2 | no eQTL | no eQTL | ||||||
| rs199528 | 44843136 | C | 17 | Intronic | WNT3 | LRRC37A2 | Temporal cortex |
3×10−6 | Decreased expression |
RP11–259G18.2 LRRC37A2 KANSL1-AS1 RP11–259G18.3 LRRC37A2 KANSL1-AS1 RP11–259G18.2 RP11–259G18.3 LRRC37A RP11–259G18.3 LRRC37A2 KANSL1-AS1 RP11–259G18.2 LRRC37A |
Anterior cingulate cortex Caudate (basal ganglia) Cerebellar hemisphere |
4×10−14
1.7×10−12 4.5×10−12 1.6×10−11 4.5×10−20 6.6×10−20 1.9×10−19 3.5×10−19 5.4×10−7 1.1×10−18 5.7×10−17 2.3×10−16 2×10−13 2×10−10 |
Decreased expression |
| rs199528 | 44843136 | C | 17 | Intronic | WNT3 | LRRC37A2 KANSL1 |
Temporal cortex Hippocampus |
3×10−6
1×10−5 |
Decreased expression |
RP11–259G18.1 MAPT-AS1 MAPT RP11–259G18.3 KANSL1-AS1 LRRC37A2 RP11–259G18.2 LRRC37A RP11–259G18.1 MAPT MAPT-AS1 SPPL2C KANSL1-AS1 RP11–259G18.3 RP11–259G18.2 LRRC37A2 KANSL1-AS1 RP11–259G18.2 LRRC37A2 RP11–259G18.3 MAPT KANSL1-AS1 RP11–259G18.3 RP11–259G18.2 LRRC37A2 KANSL1-AS1 |
Cerebellar hemisphere Cerebellum Cortex Frontal cortex Hippocampus Hypothalamus |
4.6×10−10
1.6×10−8 1.3×10−7 2×10−25 3.9×10−20 6.2×10−19 1.6×10−17 4×10−13 1.3×10−12 8.7×10−12 3.6×10−8 1.3×10−7 2.4×10−18 5.1×10−18 1.3×10−17 2.5×10−14 1.3×10−20 1.5×10−16 2.3×10−16 8.4×10−16 1.3×10−7 2.4×10−16 3.1×10−13 7×10−13 3.7×10−12 1.3×10−15 |
Decreased expression Increased expression Decreased expression Increased expression Decreased expression Increased expression Decreased expression |
| rs199528 | 44843136 | C | 17 | Intronic | WNT3 | KANSL1 | Hippocampus | 1×10−5 | Decreased expression |
LRRC37A2 RP11–259G18.3 RP11–259G18.2 LRRC37A KANSL1-AS1 RP11–259G18.3 LRRC37A2 RP11–259G18.2 RP11–259G18.1 KANSL1-AS1 RP11–259G18.3 LRRC37A2 RP11–259G18.2 LRRC37A RP11–259G18.1 |
Hypothalamus Nucleus accumbens (basal ganglia) Putamen (basal ganglia) |
7.6×10−15
1.6×10−13 5.8×10−13 5.6×10−8 1.8×10−20 1.4×10−18 4.9×10−17 3.4×10−16 7.3×10−7 2.5×10−19 6.9×10−15 3.1×10−14 9.6×10−11 1×10−6 1.6×10−6 |
Decreased expression |
| rs1358071 | 43803189 | A | 17 | Intronic | CRHR1 | LRRC37A4 | Cerebellum Frontal cortex Hippocampus Medulla Occipital cortex Putamen Substantia nigra |
7.4×10−22
1.8×10−16 3.6×10−10 4.7×10−10 5.3×10−7 2.7×10−8 1.9×10−11 5.5×10−11 2.2×10−6 7.3×10−11 2.4×10−7 |
Increased expression |
LRRC37A4P RP11–259G18.2 RP11–707O23.5 LRRC37A2 RP11–259G18.3 KANSL1-AS1 LRRC37A4P LRRC37A2 RP11–707O23.5 RP11–259G18.2 KANSL1-AS1 |
Anterior cingulate cortex Caudate (basal ganglia) |
1.9×10−11
1.6×10−9 4.3×10−9 5.3×10−8 7.5×10−7 9.7×10−7 7.3×10−15 1.7×10−14 4.5×10−13 3.1×10−12 2.8×10−11 |
Increased expression Decreased expression Increased expression Decreased expression |
| rs1358071 | 43803189 | A | 17 | Intronic | CRHR1 | LRRC37A4 KANSL1 |
Temporal cortex Thalamus White matter Hippocampus |
3.1×10−12
1.1×10−7 5.7×10−12 5.2×10−10 7.7×10−6 6.1×10−7 |
Increased expression Decreased expression |
RP11–259G18.3 LRRC37A LRRC37A4P PLEKHM1 LRRC37A2 RP11–259G18.2 RP11–259G18.3 RP11–259G18.1 KANSL1-AS1 LRRC37A RP11–798G7.5 RP11–707O23.5 FMNL1 CTD-2020K17.1 MAPT LRRC37A4P PLEKHM1 RP11–259G18.3 LRRC37A2 RP11–259G18.2 RP11–707O23.5 RP11–259G18.1 LRRC37A KANSL1-AS1 RP11–798G7.5 MAPT |
Caudate (basal ganglia) Cerebellar hemisphere Cerebellum |
1.1×10−10
6.3×10−6 1.3×10−15 4.0×10−13 2.6×10−12 1.5×10−9 1.9×10−9 2.6×10−9 6.1×10−9 2.5×10−8 5.9×10−8 2.8×10−7 4.2×10−7 5.2×10−6 6.6×10−6 5.3×10−18 4.2×10−17 5.6×10−16 3.3×10−15 6.6×10−15 2.6×10−13 1.5×10−10 1.7×10−10 7.1×10−10 1.4×10−9 5.4×10−9 |
Decreased expression Increased expression Decreased expression Increased expression Decreased expression Increased expression Decreased expression Increased expression |
| rs1358071 | 43803189 | A | 17 | Intronic | CRHR1 | KANSL1 CRHR1 |
Hippocampus Medulla |
6.1×10−7
2.9×10−6 |
Decreased expression |
MAPT-AS1 FMNL1 KANSL1-AS1 LRRC37A2 RP11–707O23.5 LRRC37A4P RP11–259G18.3 RP11–259G18.2 CRHR1-IT1 PLEKHM1 RP11–259G18.1 LRRC37A2 LRRC37A4P RP11–259G18.2 KANSL1-AS1 RP11–707O23.5 RP11–259G18.3 DND1P1 CRHR1-IT1 MAPT LRRC37A4P LRRC37A2 RP11–259G18.2 KANSL1-AS1 RP11–707O23.5 RP11–259G18.3 |
Cerebellum Cortex Frontal cortex Hippocampus |
6.2×10−8
2.7×10−6 1.5×10−14 1.6×10−11 2.7×10−11 3.2×10−11 5.7×10−11 1.3×10−10 1.3×10−8 9.4×10−7 7.8×10−6 2.5×10−11 9.3×10−11 2.2×10−10 8.2×10−10 9.8×10−10 1.7×10−9 1.6×10−6 2.7×10−6 4.1×10−6 2.0×10−12 1.6×10−11 2.7×10−11 4.1×10−11 5.8×10−11 2.5×10−8 |
Decreased expression Increased expression Decreased expression Increased expression Decreased expression Increased expression Decreased expression Increased expression Decreased expression |
| rs1358071 | 43803189 | A | 17 | Intronic | CRHR1 | CRHR1 | Medulla | 2.9×10−6 | Decreased expression |
CRHR1-IT1 DND1P1 LRRC37A2 RP11–707O23.5 KANSL1-AS1 LRRC37A4P RP11–259G18.2 RP11–259G18.3 LRRC37A4P KANSL1-AS1 RP11–707O23.5 RP11–259G18.3 LRRC37A2 RP11–259G18.2 CRHR1-IT1 LRRC37A4P LRRC37A2 KANSL1-AS1 RP11–707O23.5 RP11–259G18.3 RP11–259G18.2 CRHR1-IT1 |
Hippocampus Hypothalamus Nucleus accumbens (basal ganglia) Putamen (basal ganglia) |
4.8×10−8
2.4×10−6 1.1×10−12 3.2×10−11 8.7×10−10 1.8×10−9 2.1×10−8 2.3×10−8 2.2×10−16 2.3×10−13 1.2×10−11 4.2×10−11 5.8×10−11 8.6×10−9 1.0×10−7 2.9×10−12 1.5×10−10 2.9×10−10 1.6×10−9 4.1×10−9 1.7×10−8 5.8×10−7 |
Decreased expression Increased expression Decreased expression Increased expression Decreased expression Increased expression Decreased expression |
| rs12964543 | 56543095 | / | 18 | Intronic | ZNF532 | no eQTL | no eQTL | ||||||
| rs405509 | 45408836 | / | 19 | Intergenic | APOE | no eQTL | no eQTL | ||||||
| rs4417745 | 241225364 | / | 2 | Intergenic | OTOS | no eQTL | no eQTL | ||||||
| rs1328032 | 71420424 | / | 13 | Intergenic | DACH1 | no eQTL | no eQTL | ||||||
| rs2446406 | 51679783 | / | 15 | Intronic | GLDN | no eQTL | no eQTL | ||||||
| rs7184882 | 73737373 | C | 16 | In orf | LOC101927998 | no eQTL | no eQTL | ||||||
| rs6857 | 45392254 | T | 19 | 3′-UTR | PVRL2 | no eQTL | no eQTL | ||||||
| rs302665 | 87879627 | / | 11 | Intronic | RAB38 | no eQTL | no eQTL | ||||||
| rs10507789 | 71409940 | / | 13 | Intergenic | DACH1 | no eQTL | no eQTL | ||||||
eQTL, expression quantitative trait loci.