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. 2024 Aug 20;14(1):140. doi: 10.1038/s41408-024-01121-8

Table 2.

GeneHancer promoters and enhancers in the haplotype regions associated with the risk of MGUS, details extracted via GeneCards.

Haplotype chr: SNPa GeneHancer (GH) Identifier GH Type GH Score GH Sources Gene Association Score ENCODE transcription factor (TF) binding sites Gene Targetsc Cells and tissuesd RoadMap Epigenomicse
chr1: rs11368313 GH01J019798 Promoter/Enhancer 1.9b RefSeq, EPDnew, Ensembl, ENCODE, CraniofacialAtlas 260.60b 110 TFs 6 genes; TMCO4 B-cells, immune cells, many other cells and tissues B-cells, immune cells, many other cells
GH01J019812 Promoter/Enhancer 1.7b RefSeq, EPDnew, Ensembl, ENCODE, dbSUPER 259.30b 49 TFs 7 genes; TMCO4, RNF186, OTUD3
chr4: rs10006825 GH04J026131 Enhancer 1.1b FANTOM5, Ensembl, ENCODE 17.60b 46 TFs 6 genes; RBPJ Immune cells B-cells, T-cells, natural killer cells
chr6: rs10658790 GH06J125955 Promoter/Enhancer 2.6b RefSeq, EPDnew, FANTOM5, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 250.70b 313 TFs 7 genes; HINT3, TRMT11 B-cells, immune cells, many other cells and tissues B-cells, other immune cells, many other cells
chr10: rs10567579 GH10J132962 Promoter/Enhancer 1.4 RefSeq, Ensembl, ENCODE, CraniofacialAtlas 250.70b 20 TFs 7 genes; LINC01168, LINC01166 B-cells, immune cells, many other cells and tissues B-cells, other immune cells, many other cells
GH10J133008 Enhancer 1.3b RefSeq, ENCODE, CraniofacialAtlas, dbSUPER 29.7 43 TFs 12 genes; LINC01168 Some immune cells Monocytes, neutrophils, natural killer cells
GH10J133012 Enhancer 1.3b RefSeq, FANTOM5, ENCODE, dbSUPER 28.1 15 TFs 8 genes; LINC01168 Monocytes Monocytes, neutrophiles, natural killer cells
chr11: rs106282082 GH11J134729 Enhancer 0.8b RefSeq, ENCODE, dbSUPER 256.80b 4 TFs 5 genes; LINC02714
chr17: rs111362005 GH17J000914 Enhancer 1.5b RefSeq, FANTOM5, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 6.40b 17 TFs 7 genes; NXN Neutrophils, some other cells and tissues Neutrophils, some other cells
GH17J000924 Promoter/Enhancer 1.8b RefSeq, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 17.90b 162 TFs 12 genes; NXN Some cells and tissues Some cells
GH17J000931 Promoter/Enhancer 1.6b Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 29.60b 122 TFs 12 genes; NXN Some cells and tissues
chr17: rs1024819 GH17J057521 Enhancer 1.6b RefSeq, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 0.06 114TFs 9 genes; MSI2 B-cells, immune cells; SE_13320 (CD34 primary cells); many other cells and tissues B-cells, some other immune cells, some other cells
chr17: rs10163481 GH17J077084 Enhancer 0.4b Ensembl, ENCODE, dbSUPER 255.60b no 6 genes; SNHG20
GH17J077087 Promoter/Enhancer 2.5b RefSeq, EPDnew, FANTOM5, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 250.70b 263TFs 10 genes; SEC14L1, SNHG20 B-cells, immune cells B-cells, other immune cells, many other cells
GH17J077095 Enhancer 1.3b FANTOM5, Ensembl, ENCODE, dbSUPER 26.60b 83 TFs 8 genes; SEC14L1, SNHG20 Immune cells Immune cells, many other cells
GH17J077106 Promoter/Enhancer 1.9b RefSeq, FANTOM5, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 18.50b 121 TFs 10 genes; SEC14L1 B-cells, lymphocyte of B lineage, immune cells B-cells, other immune cells, many other cells
GH17J077114 Promoter/Enhancer 2.0b RefSeq, FANTOM5, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 10.20b 233 TFs 9 genes; SEC14L1 B-cells, immune cells B-cells, immune cells, many other cells
GH17J077137 Promoter/Enhancer 2.6b RefSeq, EPDnew, FANTOM5, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 259.8b 300 TFs 12 genes; SEC14L1 B-cells, immune cells, other cells B-cells, immune cells, many other cells
GH17J077150 Enhancer 0.3b ENCODE, dbSUPER 7.20b no 7 genes; SEC14L1
GH17J077152 Enhancer 0.3b ENCODE, dbSUPER 7.20b no 6 genes; SEC14L1
GH17J077159 Promoter/Enhancer 1.2b RefSeq, ENCODE, dbSUPER 7.20b 54 TFs 7 genes; SEC14L1 B-cells B-cells, immune cells, some other cells
chr19: rs10420324 GH19J053864 Promoter/Enhancer 2.6b RefSeq, EPDnew, FANTOM5, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 265.10b 255 TFs 39 genes; MYADM, ZNF765, ZNF813, ZNF761, CNOT3, PRKCG B-cells, immune cells; SE_20401 (CD56 primary cells), SE in many immune cells B-cells, immune cells, many other cells
GH19J053874 Enhancer 0.6b ENCODE, dbSUPER 11.00b 5 TFs 6 genes; MYADM B-cells, immune cells; SE_20401 (CD56 primary cells), SE in many immune cells B-cells, immune cells
GH19J053877 Enhancer 0.6b ENCODE, dbSUPER 6.90b 5 TFs 10 genes; PRKCG B-cells; SE in some immune cells Many cells
GH19J053889 Enhancer 0.8b ENCODE, dbSUPER 18.50b 24 TFs 6 genes; MYADM Immune cells B-cells, monocytes, natural killer cells
GH19J053907 Promoter/Enhancer 1.2b FANTOM5, Ensembl, ENCODE 260.40b 31 TFs 8 genes; CACNG7, PRKCG, CACNG8
GH19J053956 Promoter/Enhancer 1.8b RefSeq, EPDnew, FANTOM5, Ensembl, ENCODE 260.40b 54 TFs 23 genes; CACNG8, CACNG7
GH19J053977 Promoter/Enhancer 1.5b RefSeq, Ensembl, ENCODE 18.50b 149 TFs 27 genes; CACNG8 B-cells, immune cells Some cells
chr20: rs1051904 GH20J004133 Enhancer 1.7b efSeq, FANTOM5, Ensembl, ENCODE, dbSUPER 3.00b 149TFs 10 genes; SMOX Monocytes, neutrophils, other cells and tissues Some cells
GH20J004148 Promoter/Enhancer 2.0b RefSeq, EPDnew, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 268.70b 83 TFs 6 genes; SMOX Immune cells, many other cells
GH20J004159 Enhancer 1.2b RefSeq, FANTOM5, ENCODE, dbSUPER 8.60b 20 TFs 6 genes; SMOX Monocytes B-cells, other immune cells, many other cells
GH20J004165 Enhancer 1.5b RefSeq, FANTOM5, ENCODE, CraniofacialAtlas, dbSUPER 20.7b 36 TFs 9 genes; SMOX Some cells
GH20J004169 Promoter/Enhancer 2.1b RefSeq, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 7.90b 190 TFs 7 genes; SMOX B-cells, immune cells B-cells, other immune cells, many other cells
chr20: rs111797554 GH20J057617 Promoter/Enhancer 2.0b RefSeq, EPDnew, FANTOM5, Ensembl, ENCODE, dbSUPER 264.30b 67 TFs 4 genes; ZBP1 B-cells, immune cells; SE_20522 (CD56 primary cells), SE_16712 (CD4 naive primary cells) B-cells, immune cells, gastrointestinal tract
GH20J057627 Enhancer 1.1b FANTOM5, ENCODE, CraniofacialAtlas, dbSUPER 11.90b 13 TFs 8 genes; ZBP1 B-cells, immune cells; SE_20522 (CD56 primary cells), SE_16712 (CD4 naive primary cells) B-cells, other immune cells, many other cells
chr 22: rs1045588 GH22J017767 Enhancer 1.2b RefSeq, ENCODE, dbSUPER 4.90b 49 TFs 4 genes; BID Immune cells; SE_09461 (CD14+ monocytes) B-cells, other immune cells, some other cells
GH22J017769 Promoter/Enhancer 2.5b RefSeq, EPDnew, FANTOM5, Ensembl, ENCODE, CraniofacialAtlas, dbSUPER 264.80b 155 TFs 7 genes; BID B-cells, immune cells; SE_09461 (CD14+ monocytes); many cells and tissues B-cells, other immune cells, many other cells
GH22J017784 Enhancer 1.8b RefSeq, VISTA, ENCODE, CraniofacialAtlas, dbSUPER 0.41 153 TFs 8 genes B-cells, immune cells; SE_09461 (CD14+ monocytes) Immune cells, many other cells
GH22J017794 Enhancer 1.6b RefSeq, FANTOM5, Ensembl, ENCODE, dbSUPER 15.80b 83 TFs 10 genes; BID, MICAL3 B-cells, immune cells; SE_09461 (CD14+ monocytes) B-cells, monocytes, hematopoietic stem cells, natural killer cells

aHaplotype identified by the chromosome and the joint SNP in the haplotype region.

bDouble Elite GeneHancer score and Gene association score.

cNumber of gene targets; Gene targets in the haplotype region.

dExamples of tissues, in which the promoter/enhancer is active in GeneHancer sources; Superenhancer (SE) in B-cells or immune cells.

eCell populations with active chromatin state in 6 immune cell populations and over 10 adult cell and tissue types were extracted via Roadmap Epigenomics.