Table 1.
GWAS Locus | Sentinel SNP | Proxy SNP (r2) | Implicated genes (FPKM) | GWAS Set |
---|---|---|---|---|
ANKFN1 | rs72829754 | rs56335503 (0.96), rs8065311 (0.95) | NOG (21.00) | Heel |
C11orf58 | rs56928337 | rs78152188 (0.99) | TCONS_00019584 (NA), TCONS_00019858 (NA) | Heel |
CCND1 | rs4980659 | rs6606645 (0.91) | CCND1 (88.53) | DEXA |
CRADD | rs7969076 | rs7953280 (0.88) | SOCS2 (3.78), SOCS2-AS1 (0.59) | Heel |
DLX5 | rs1724298 | rs1724298 (1) | SHFM1 (9.38) | Heel |
DLX6-AS1 | rs17598132 | rs73402679 (0.94) | SHFM1 (9.38) | Heel |
DNM3 | rs12041600 | rs1992549 (1), rs1992550 (1), rs2586393 (0.99), rs6694387 (0.94) | DNM3OS (8.92), MIR199A2 (NA) | Heel |
EMP1 | rs76243438 | rs116942315 (1), rs117604090 (1), rs199595633 (1), rs75180224 (1) | EMP1 (30.57) | Heel |
EN1 | rs62159864 | rs62159869 (0.97) | TCONS_00004419 (NA) | Heel |
EPDR1 | rs1717731 | rs939666 (0.87) | EPDR1 (25.59), SFRP4 (0.88) | Heel |
FADS2 | rs174574 | rs3834458 (0.92) | FADS1 (19.09) | Heel |
FRZB | rs10206992 | rs36090522 (0.99), rs9288087 (0.99) | FRZB (12.92) | Heel |
GMDS-AS1 | rs4959677 | rs1010762 (0.85) | LINC01600 (NA), TCONS_00011252 (NA) | Heel |
GNG12-AS1 | rs143243230 | rs143243230 (1) | WLS (12.78) | Heel |
HOXA-AS3 | rs62454420 | rs62454420 (1) | CBX3 (15.70), SKAP2 (5.32) | Heel |
HOXA11 | rs17501090 | rs149457254 (0.82) | HIBADH (10.12), TAX1BP1 (9.35) | Heel |
HOXC6 | rs736825 | rs765634 (0.88) | HOXC-AS1 (0.34), HOXC4 (0.15), HOXC5 (0.36), HOXC9 (8.71), SMUG1 (5.16), TCONS_00020435 (0.02), TCONS_00020436 (NA), TCONS_00020437 (0.01), TCONS_00020438 (NA) | DEXA |
IGFBP7 | rs11133474 | rs11133472 (0.99), rs11133474 (1) | IGFBP7 (1445.99), IGFBP7-AS1 (0.58) | Heel |
JAG1 | rs17457340 | rs141094380 (0.95), rs78438678 (0.95) | LOC339593 (NA), TCONS_l2_00016479 (NA), TCONS_l2_00016480 (NA), TCONS_l2_00016851 (0.01) | Heel |
KCNE2 | rs55787537 | rs55787537 (1) | LINC00649 (0.02), TCONS_00029004 (NA) | Heel |
KIAA2012 | rs62195575 | rs13000317 (0.82), rs13384015 (0.87) | CDK15 (0.09), KIAA2012 (NA) | Heel |
KIAA2018 | rs1026364 | rs150722690 (0.90), rs150722690 (0.86), rs16861312 (0.90), rs9288983 (0.90), rs9851731 (0.87) | ATP6V1A (21.00), NAA50 (13.11) | DEXA |
LEKR1 | rs344081 | rs344088 (0.97) | SSR3 (60.86), TIPARP (11.64), TIPARP-AS1 (0.15) | DEXA |
LINC00880 | rs56082403 | rs13322435 (0.98), rs56406311 (0.9), rs9817452 (0.9), rs9854955 (0.98) | LEKR1 (0.08), LINC00886 (0.55), SSR3 (60.86), TCONS_00006285 (NA), TCONS_l2_00019596 (0.03), TIPARP (11.64), TIPARP-AS1 (0.15) | Heel |
LOC101929268 | rs6471752 | rs72639005 (0.84), rs55864946 (0.84), rs72639011 (0.84), rs72639012 (0.84) | LOC101929217 (NA), SNAI2 (39.39), TCONS_00014692 (0.01) | Heel |
MAPT/WNT3 | rs1864325 | 17:44121917:C:T (0.99), 17:44231617:A:T (0.99), 17:44237372:G:C (0.99), 17:44245359:G:A (0.84), rs62063683 (0.99), rs974291 (0.99), rs974292 (0.99) | KANSL1 (1.89), KANSL1-AS1 (0.71) | DEXA |
MED13L | rs73200209 | rs17498543 (0.84) | MIR4472–2 (NA) | DEXA |
MEPE | rs6532023 | rs1471401 (1) | SPP1 (12.86) | Both |
MLPH | rs58057291 | rs13408361 (0.9), rs6722471 (0.93), rs7569197 (0.9), rs7571898 (0.9), rs7598954 (0.87), rs9287620 (0.87) | COL6A3 (125.76), TCONS_00003518 (NA) | Heel |
MTAP | rs7035284 | rs7852691 (0.98) | MIR31HG (9.48) | DEXA |
PHLDB1 | rs10790255 | rs10892247 (0.85) | PHLDB1 (11.37) | Heel |
PLEKHG4 | rs17680862 | rs8047360 (0.8), rs8050375 (0.8), rs114485334 (0.83) | B3GNT9 (27.79), CES4A (0.22), FBXL8 (2.05), TRADD (11.46) | Heel |
RERE | rs2252865 | rs2708633 (0.92), rs301789 (0.93), rs301790 (0.93), rs301791 (0.93), rs301792 (0.93) | LOC102724552 (NA), RERE (0.94) | DEXA |
RNU5F-1 | rs2275707 | rs1694593 (0.96), rs1694594 (0.96) | SLC30A10 (0.00) | Heel |
SFRP4 | rs17236800 | rs10264106 (1), rs1014939 (0.99), rs2167269 (0.99) | STARD3NL (6.44), TRG-AS1 (NA) | Both |
SLC1A3 | rs1428968 | rs1428968 (1) | SLC1A3 (0.78) | Heel |
SLC8A1 | rs10490046 | rs10490046 (1) | SLC8A1 (3.39) | Both |
SLX4IP | rs6040006 | rs111539884 (0.88), rs74516716 (0.88), rs78532542 (0.88) | LOC339593 (NA), TCONS_l2_00016479 (NA), TCONS_l2_00016480 (NA), TCONS_l2_00016851 (0.01) | Heel |
SMAD3 | rs1545161 | rs1545161 (1), rs28587205 (0.98), rs72219900 (0.99) | SMAD3 (2.59) | Both |
SMAD9 | rs556429 | rs17217404 (0.95) | SMAD9 (11.59) | DEXA |
SMG6 | rs35401268 | rs35401268 (1) | SMG6 (3.19) | Both |
SPEN | rs6701290 | rs6688051 (0.93) | FLJ37453 (NA), SPEN (1.15), ZBTB17 (6.09) | Heel |
SPTB | rs1957429 | rs28370916 (0.83) | SPTB (0.02) | DEXA |
STARD3NL | rs6956946 | rs1524068 (1), rs940347 (1) | EPDR1 (25.59), SFRP4 (0.88) | Both |
TBPL2 | rs34652660 | rs12431542 (0.90), rs202007979 (0.89), rs4901570 (0.90), rs8009706 (0.90) | KTN1 (10.46), KTN1-AS1 (0.03) | DEXA |
WLS | rs17482952 | rs17482952 (1), rs79441491 (0.97) | WLS (12.78) | DEXA |
For each locus, proxy SNPs in open chromatin looping to an open promoter are reported, together with their sentinel SNPs and the associated GWAS loci. Looping interactions and open chromatin maps were derived from promoter-focused Capture C and ATAC-seq experiments on hMSC-derived osteoblasts cultures from 3 or more individuals. Average expressions (in FPKM) of the target genes in hMSC-derived osteoblasts from RNA-seq experiments from the same 3 individuals are also reported.