Table 4 eQTL genes in TAD
From: Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping
SNP | Chromosome | Base-pair position | #eQTL genes | SK-N-SH | U-251MG | ||||
|---|---|---|---|---|---|---|---|---|---|
#eQTL genes in TAD | Proportion of eQTL genes in TAD (%) | eQTL genes in TAD | #eQTL genes in TAD | Proportion of eQTL genes in TAD (%) | eQTL genes in TAD | ||||
rs4038131 | 2 | 17775032 | 1 | 0 | 0.0 | - | 0 | 0.0 | - |
rs4663105 | 2 | 127891427 | 1 | 1 | 100.0 | BIN1 | 1 | 100.0 | BIN1 |
rs75847378 | 2 | 40181517 | 1 | 1 | 100.0 | SLC8A1-AS1 | 1 | 100.0 | SLC8A1-AS1 |
rs6448799 | 4 | 11630049 | 1 | 0 | 0.0 | - | 1 | 100.0 | HS3ST1 |
rs11168036 | 5 | 139707439 | 5 | 3 | 60.0 | CYSTM1,PFDN1,SLC4A9 | 3 | 60.0 | CYSTM1,PFDN1,SLC4A9 |
rs185968827 | 6 | 56708510 | 2 | 2 | 100.0 | BEND6,DST | 2 | 100.0 | BEND6,DST |
rs1476679 | 7 | 100004446 | 23 | 16 | 69.6 | AGFG2,AP4M1,GAL3ST4,GATS,LAMTOR4,MCM7,MIR106B,MIR25,MIR93,NYAP1,PILRA,PILRB,PVRIG,STAG3,TAF6,ZSCAN21 | 6 | 26.1 | ACHE,ACTL6B,AGFG2,GIGYF1,NYAP1,TRIM56 |
rs1532278 | 8 | 27466315 | 1 | 1 | 100.0 | CLU | 1 | 100.0 | CLU |
rs9331888 | 8 | 27468862 | 1 | 1 | 100.0 | EPHX2 | 1 | 100.0 | EPHX2 |
rs1582763 | 11 | 60021948 | 1 | 1 | 100.0 | MS4A6A | 1 | 100.0 | MS4A6A |
rs573521 | 11 | 102716980 | 1 | 1 | 100.0 | MMP1 | 1 | 100.0 | MMP1 |
rs249153 | 12 | 95324389 | 1 | 1 | 100.0 | VEZT | 1 | 100.0 | VEZT |
rs56146971 | 14 | 91920101 | 1 | 1 | 100.0 | TC2N | 1 | 100.0 | TC2N |
rs111816999 | 17 | 6882443 | 2 | 0 | 0.0 | - | 1 | 50.0 | TNK1 |
rs117964204 | 17 | 48692082 | 1 | 1 | 100.0 | SPATA20 | 1 | 100.0 | SPATA20 |
rs7225151 | 17 | 5137047 | 9 | 8 | 88.9 | C17ORF107,CAMTA2,CHRNE,LOC100130950,NUP88,RABEP1,SCIMP,ZNF232 | 8 | 88.9 | C17ORF107,CAMTA2,CHRNE,LOC100130950,NUP88,RABEP1,SCIMP,ZNF232 |
rs4147929 | 19 | 1063443 | 3 | 3 | 100.0 | ABCA7,ARHGAP45,POLR2E | 3 | 100.0 | ABCA7,ARHGAP45,POLR2E |
rs439401 | 19 | 45414451 | 2 | 2 | 100.0 | APOC1,APOE | 2 | 100.0 | APOC1,APOE |
rs7364180 | 22 | 42218856 | 25 | 15 | 60.0 | CSDC2,CYP2D6,CYP2D7,MEI1,MIR33A,NAGA,NDUFA6,NFAM1,PMM1,POLR3H,SMDT1,SNU13,SREBF2,TCF20,WBP2NL | 12 | 48.0 | CYP2D6,CYP2D7,MEI1,MIR33A,NAGA,NDUFA6,NFAM1,SMDT1,SNU13,SREBF2,TCF20,WBP2NL |