Table 1

The associations of individual SNPs (used as genetic instruments in MR analyses) with the relevant liver function markers in UCLEB studies, Fenland study, and GWAS

SNPLiver function markerLocus*Effect size in SD units in UCLEB studies (95% CI)Effect size in SD units in Fenland study (95% CI)Effect size in SD units from published GWAS (95% CI)
rs6834314ALTHSD17B13, MAPK100.05 (0.01, 0.09)0.05 (0.02, 0.07)0.06 (0.04, 0.08)
rs11597390ALTCPN10.09 (0.05, 0.13)0.03 (0.01, 0.06)0.04 (0.03, 0.06)
rs2143571ALTSAMM500.14 (0.09, 0.19)0.07 (0.04, 0.12)0.09 (0.07, 0.11)
rs2954021ALTTRIB1n0.03 (−0.01, 0.07)0.02 (−0.00, 0.04)0.04 (0.02, 0.05)
rs17109512ASTGOT1−0.04 (−0.18, 0.11)N/A0.03 (−0.05, 0.1)
rs738407ASTPNPLA30.13 (0.08, 0.19)N/A0.09 (0.06, 0.12)
rs738408ASTPNPLA30.12 (0.08, 0.17)N/A0.19 (0.16, 0.22)
rs1780324ALPNBPF3-ALPL0.07 (0.02, 0.12)0.08 (0.05, 0.10)0.09 (0.07, 0.11)
rs16856332ALPABCB11−0.02 (−0.20, 0.15)0.06 (−0.01, 0.13)0.14 (0.09, 0.19)
rs9467160ALPGPLD10.06 (0.01, 0.12)0.10 (0.07, 0.13)0.1 (0.08, 0.13)
rs514708ALPABO0.06 (0.00, 0.12)0.08 (0.05, 0.11)0.1 (0.08, 0.13)
rs2236653ALPST3GAL40.01 (−0.05, 0.07)0.07 (0.04, 0.10)0.06 (0.04, 0.08)
rs7186908ALPHPR, PMFBP1−0.02 (−0.09, 0.05)0.02 (−0.01, 0.05)0.07 (0.05, 0.1)
rs7267979ALPABHD12, GINS1, PYGB0.03 (−0.02, 0.08)0.07 (0.04, 0.10)0.05 (0.03, 0.07)
rs281377ALPABO0.00 (−0.05, 0.06)0.06 (0.04, 0.09)0.07 (0.05, 0.09)
rs314253ALPASGR1o, DLG4n0.02 (−0.04, 0.07)0.04 (0.01, 0.07)0.08 (0.06, 0.1)
rs579459ALPABO0.08 (0.02, 0.14)0.25 (0.22, 0.28)0.31 (0.28, 0.34)
rs6984305ALPPPP1R3B−0.03 (−0.11, 0.05)0.08 (0.04, 0.12)0.1 (0.07, 0.13)
rs7923609ALPJMJD1Cnce, NRBF2e0.05 (0.00, 0.10)0.09 (0.06, 0.11)0.08 (0.06, 0.1)
rs174601ALPC11orf10e, FADS1e, FADS2ne−0.00 (−0.06, 0.05)0.06 (0.03, 0.08)0.06 (0.04, 0.09)
rs2954021ALPTRIB10.07 (0.01, 0.12)0.04 (0.01, 0.06)0.05 (0.03, 0.07)
rs10819937ALPALDOBo, C9orf125nNot in UCLEB0.06 (0.02, 0.09)0.09 (0.06, 0.12)
rs1497406GGTRSG1, EPHA20.05 (0.01, 0.09)0.07 (0.04, 0.09)0.06 (0.04, 0.07)
rs12145922GGTCCBL2, PKN2−0.02 (−0.05, 0.02)0.01 (−0.02, 0.03)0.04 (0.03, 0.06)
rs1335645GGTCEPT1, DENND2DNot in UCLEB0.03 (−0.01, 0.07)0.07 (0.04, 0.09)
rs10908458GGTDPM3, EFNA1, PKLR0.04 (0.01, 0.07)0.05 (0.02, 0.07)0.06 (0.04, 0.07)
rs13030978GGTMYO1B, STAT40.07 (0.02, 0.12)0.03 (0.01, 0.06)0.06 (0.04, 0.08)
rs2140773GGTEFHD1, LOC100129166−0.01 (−0.04, 0.03)0.02 (−0.01, 0.04)0.05 (0.03, 0.06)
rs4547811GGTZNF8270.08 (0.03, 0.13)0.09 (0.06, 0.12)0.1 (0.08, 0.12)
rs4074793GGTITGA10.14 (0.07, 0.20)0.07 (0.02,0.11)0.08 (0.05, 0.12)
rs9296736GGTMLIP0.03 (0.00, 0.07)0.04 (0.02, 0.07)0.05 (0.03, 0.06)
rs754466GGTDLG5Not in UCLEB0.07 (0.04, 0.10)0.05 (0.03, 0.07)
rs8038465GGTNPTN -CD2760.04 (−0.00, 0.09)0.00 (−0.02, 0.03)0.04 (0.02, 0.05)
rs4581712GGTDYNLRB20.09 (−0.00, 0.18)0.07 (0.04, 0.10)0.05 (0.03, 0.07)
rs1076540GGTMICAL30.05 (0.01, 0.09)0.06 (0.03, 0.09)0.07 (0.06, 0.09)
rs2739330GGTDDT, DDTL, GSTT1, GSTT2BMIF0.06 (0.02, 0.10)0.03 (0.01, 0.06)0.06 (0.04, 0.08)
rs4820599GGTGGT10.13 (0.10, 0.17)0.09 (0.06, 0.12)0.13 (0.11, 0.15)
rs10513686GGTSLC2A2nc0.06 (0.01, 0.11)0.04 (0.01, 0.08)0.08 (0.05, 0.1)
rs1260326GGTC2orf16e, GCKRnc0.03 (−0.00, 0.06)0.05 (0.02, 0.07)0.05 (0.03, 0.07)
rs17145750GGTMLXIPLnce0.08 (0.03, 0.12)0.07 (0.03, 0.10)0.07 (0.04, 0.1)
rs339969GGTRORAn0.05 (0.02, 0.09)0.05 (0.03, 0.08)0.07 (0.05, 0.09)
rs516246GGTFUT20.04 (0.01, 0.07)0.04 (0.01, 0.06)0.04 (0.02, 0.05)
rs7310409GGTHNF1Anc, C12orf27e0.11 (0.08, 0.15)0.10 (0.08, 0.13)0.1 (0.09, 0.12)
rs944002GGTC14orf73nc0.12 (0.08, 0.15)0.09 (0.06, 0.12)0.1 (0.08, 0.12)
rs6888304GGTCDH6nNot in UCLEB0.05 (0.02, 0.08)0.04 (0.02, 0.06)
rs9913711GGTFLJ37644e, SOX9nNot in UCLEB0.05 (0.03, 0.08)0.04 (0.02, 0.05)
rs12968116GGTATP8B1ncgNot in UCLEB0.05 (0.01, 0.09)0.07 (0.04, 0.1)
rs4503880GGTNEDD4LnNot in UCLEB0.07 (0.04, 0.10)0.06 (0.03, 0.08)
  • N/A, not applicable.

  • *Mapped gene for each SNP is given as reported in the original GWAS publication.

  • †All SNP–liver function marker associations in the UCLEB studies and the Fenland study were adjusted for age and sex (if relevant). Individual study estimates in UCLEB were combined using fixed-effect meta-analyses.

  • ‡Effect sizes extracted from Chambers et al., 2011 (28). GWAS effect sizes for ALT, ALP, and GGT were converted to SD units using the median SD from the UCLEB and Fenland studies.