Skip to main content

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