Table 1.
T1D 3DFAACTS SNPs identified using the 3DFAACTS-SNP filtering workflow from T1D fine-mapping SNPs
| Chromosome | Position | SNP id | Nearest locus (linear distance) | Located within regulatory regions | Interacting genes (3D) | |
|---|---|---|---|---|---|---|
| Treg ChromHMM | FANTOM5 expressed enhancers | |||||
| chr2 | 204700689 | rs12990970 | CTLA4 | TssAFlnk | CD28,CTLA4,ICOS | |
| 204732714 | rs231775 | TssAFlnk | RAPH1,CD28,ICOS | |||
| 204738919 | rs3087243 | EnhG | RAPH1 | |||
| chr3 | 46327588 | rs11718385 | CCR3 | Enh | XCR1,CCR2,CCR5AS,CCR5 | |
| 46391390 | rs6441972 | CCR2 | TssAFlnk | CCR3 | ||
| 46401032 | rs3138042 | Enh | ||||
| 46411661 | rs2856758 | CCR5 | Enh | SLC6A20,FYCO1,CXCR6,XCR1, LOC105377067,CCR3,CCR1,CCR2 | ||
| 46412259 | rs1799988 | TssAFlnk | SLC6A20, FYCO1,CXCR6, XCR1, LOC105377067,CCR3,CCR1,CCR2 | |||
| chr5 | 35852311 | rs6890853 | IL7R | TssAFlnk | SPEF2,LOC105374724,CAPSL | |
| chr6 | 90948476 | rs62408222 | BACH2 | Enh | BACH2,LOC105377891 | |
| 90983850 | rs905671 | Enh | ✓ | BACH2 | ||
| 90984035 | rs943689 | Enh | ✓ | BACH2 | ||
| 90995980 | rs614120 | TssAFlnk | ✓ | BACH2,LOC105377891 | ||
| chr7 | 50462418 | rs10216316 | IKZF1 | EnhG | SPATA48 | |
| 50462498 | rs10215297 | EnhG | SPATA48 | |||
| 50465206 | rs55981617 | EnhG | SPATA48,ZPBP,IKZF1 | |||
| 50465654 | rs12670555 | EnhG | SPATA48,ZPBP,IKZF1, | |||
| chr10 | 6088743 | rs12722508 | IL2RA | TssAFlnk | RMB17 | |
| 6094697 | rs61839660 | TssAFlnk | IL2RA,RMB17,PFKFB3,LINC02649 | |||
| 6096667 | rs12722496 | ✓ | IL2RA,RBM17,PFKFB3,LINC02649 | |||
| 6107534 | rs11597367 | Enh | IL2RA,RBM17 | |||
| chr12 | 9910720 | rs3176793 | CD69 | TssA | LOC374443,CLEC2D | |
| 9912182 | rs2160086 | TssA | LOC374443,CLEC2D | |||
| 9912730 | rs3176789 | TssA | LOC374443,CLEC2D,LOC105369728 | |||
| 9916640 | rs3136559 | Enh | LOC374443,CLEC2D,LOC105369728 | |||
| 9925758 | rs1029992 | Enh | ||||
| 9926064 | rs1029991 | Enh | ||||
| 9926397 | rs1029990 | Enh | ✓ | |||
| 9926624 | rs10844749 | Enh | ||||
| 9926784 | rs1540356 | Enh | ||||
| chr15 | 38903672 | rs16967112 | RASGRP1 | Enh | ✓ | FAM98B,RASGRP1,LOC105370775, LOC105370780,LINC02694,FSIP1 |
| 38903884 | rs56249992 | Enh | RASGRP1,FAM98B, LOC105370775, LOC105370780,LINC02694,FSIP1 | |||
| chr16 | 11188949 | rs71136618 | CLEC16A | Enh | CLEC16A,LOC107984859, LOC105371082,RMI2,SOCS1 | |
| chr17 | 38755665 | rs11656173 | SMARCE1 | Enh | ✓ | CCR7 |
| chr18 | 12838767 | rs17657058 | PTPN2 | Enh | LINC01882,PTPN2,SEH1L | |
| chr22 | 30581722 | rs5753037 | HORMAD2 | Enh | HORMAD2,LIF-AS1,LIF | |
The nearest locus indicates the closest gene to the variants in linear distance, while 3D interacting genes are genes in contact with the variants via Treg Hi-C interactions. Overlapped regulatory elements of each 3DFAACTS SNPs are displayed, including chromatin states from a 15-state model and expressed enhancers from FANTOM5. Detailed SNP and interaction information is contained in Additional file 3: Table S3
*Genes in bold indicate novel 3D interacting genes of the identified SNPs