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. 2023 Dec 4;56(1):37–50. doi: 10.1038/s41588-023-01600-x

Table 1.

Genetic regions associated with whole-blood perturbation response traits

Lead SNP rsID P value Candidate genes CADD consequence Top trait Obs. Previous association
1:20032226:G:A rs10917522 3.09 × 10−9 TMCO4 Intron WDF Empa 1.5 h NE3 CV SFL 380 –
1:25703156:C:T rs644592 5.58 × 10−18 RHCE Intron RET rotenone 6 h ov. RET1 CV SFL 943 RBCa
1:89840389:T:C rs7550358 1.55 × 10−8 GBP6 Intron RET captopril 5.5 h RET2 Count 353 –
1:103361529:A:C rs72683260 3.22 × 10−9 COL11A1 Intron RET TMAO 3.5 h RBC2 Med SFL 361 –
1:225579918:A:T rs41268717 6.90 × 10−9 DNAH14, LBR Intron WNR water 15 h WBC2 Med FSC 1,423 RBCa
1:248039451:C:T rs3811444 1.37 × 10−11 TRIM58 Missense RET KCl 17 h RET1 SD SSC 1,410 RBCa, PLTb
2:203226371:G:A rs72925015 1.24 × 10−8 BMPR2 Upstream WDF water 15 h MO2 Med SSC 1,392 RBCa
3:16551213:C:G rs2881513 3.78 × 10−8 RFTN1 Regulatory, intron WNR nigericin 0.5 h UK1 CV FSC 327 –
3:49774658:G:A rs73077175 1.01 × 10−13 CDHR4-UBA7, IP6K1 Intron WDF baseline NE2 Med SFL 1,629 RBCa
3:50255663:C:T rs35926495 8.32 × 10−25 SLC38A3 Intron WDF baseline NE2 Med SFL 1,664 RBCa
3:50374293:A:G rs2073499 9.63 × 10−9 HYAL3, RASSF1 Regulatory, intron WDF baseline NE2/NE4 ratio 1,565 BASOa
3:51406862:A:G rs111614418 2.29 × 10−8 DOCK3 Intron WNR LPS 18 h WBC Med SSC 1,416 EOb
3:56849749:T:C rs1354034 7.23 × 10−10 ARHGEF3 Intron RET KCl 17 h PLT Med SFL 1,397 PLT, RBC, LYb
3:94702472:C:T rs1432474 1.92 × 10−8 LINC00879 Intron WDF water 23 h MO2 CV FSC 1,415 –
4:38677227:A:C rs34089598 7.94 × 10−12 KLF3, KLF3-AS1 Regulatory, intron WNR Pam3CSK4 19 h WBC CV FSC 1,310 WBCb
4:38798648:C:A rs5743618 8.20 × 10−103 TLR1, TLR6, TLR10 Missense WDF Pam3CSK4 19 h NE1 Med FSC 1,300 –
4:178716833:T:C rs10030190 4.08 × 10−8 LINC01098 Intron WNR baseline UK1 CV FSC 1,486 –
4:185602707:G:A rs72703519 2.92 × 10−20 CASP3-ACSL1 Intron WDF KCl 17 h NE2/NE4 ratio 1,336 –
4:185665118:G:A rs12513029 1.55 × 10−13 CASP3-ACSL1 Intergenic WDF colchicine 20 h NE4 SD SFL 1,296 PLTa
6:25719210:T:C rs9358870 3.71 × 10−9 SCGN Intergenic RET DMSO 4.5 h RBC1 SD FSC 355 PLTb
6:25878848:A:G rs55925606 2.97 × 10−9 HFE-TRIM38 Upstream and downstream RET DMSO 4.5 h RBC1 CV FSC 381 RBC, PLTb
7:18398911:C:T rs62450075 9.82 × 10−9 HDAC9 Intron RET KCl 17 h RBC1 SD FSC 1,381 –
7:24832308:A:G rs4719781 2.50 × 10−18 DFNA5, OSBPL3 Downstream WNR ciprofloxacin 22 h BASO Med SSC 1,260 –
7:28773957:A:C rs73075771 1.19 × 10−8 CREB5 Intron WNR TMAO 3.5 h UK1 CV SSC 325 WBCb
7:92408370:C:T rs445 2.30 × 10−14 CDK6 Regulatory, intron WDF baseline EO1 Med SSC 1,698 WBC, RBCb
7:128371246:C:T rs41274144 6.64 × 10−9 GARIN1B 3′ UTR WNR TMAO 3.5 h PLT CV SSC 327 –
8:4096691:T:C rs28522529 2.87 × 10−10 CSMD1 Intron WDF captopril 5.5 h MO2 CV SFL 343 –
8:6828115:G:T rs2615764 1.89 × 10−17 DEFA10P Upstream PLT-F baseline WBC1 Med SSC 1,662 WBCb
9:7015133:A:G rs10975974 3.39 × 10−10 KDM4C Intron WDF baseline MO2 Med SSC 1,688 RBCa
9:9744225:A:C rs80353904 3.10 × 10−8 PTPRD Intron WDF nigericin 7.5 h EO2 CV SSC 351 –
10:3139540:A:G rs34538474 6.55 × 10−15 PFKP Intron WDF KCl 17 h NE2/NE4 ratio 1,339 PLTa
10:71109406:T:C rs6480404 4.03 × 10−13 HK1 Regulatory, intron WDF Alhydrogel 21 h NE4 SD SFL 1,378 RBCb
11:972270:C:T rs7933889 1.03 × 10−8 AP2A2 Intron WNR ciprofloxacin 22 h WBC2 SD SFL 1,358 –
11:11548147:A:G rs10831631 3.19 × 10−9 GALNT18 Intron WDF LiCL 4 h NE1 CV FSC 369 –
11:56806558:C:T rs12421419 4.11 × 10−9 OR5AK2, OR5AK4P Downstream WDF colchicine 20 h LY SD SSC 1,338 –
11:57159189:T:C rs548854 1.81 × 10−12 PRG2, SLC43A3 Upstream, intron WDF colchicine 20 h EO1 Med FSC 1,383 –
11:87048905:G:A rs4536247 9.81 × 10−9 TMEM135 Intergenic WDF water 15 h NE2% 1,358 –
11:93862020:C:T rs4753126 3.58 × 10−12 HEPHL1, PANX1 Regulatory, upstream WDF colchicine 20 h EO2 Med SFL 1,319 RBCa
11:112971545:C:T rs11214488 2.16 × 10−8 NCAM1 Intron WDF cholic acid 6.5 h NE3 CV SSC 360 –
12:75695577:A:G rs10785185 2.62 × 10−8 CAPS2 Intron PLT-F isobutyric 3 h IPF SD FSC 370 –
12:122399173:C:A rs11615667 1.24 × 10−9 WDR66 Intron PLT-F ciprofloxacin 22 h IPF SD SFL 1,284 PLTa
14:21347966:G:T rs74034667 1.88 × 10−10 RNASE3 Upstream WDF baseline MO2 CV SFL 1,700 –
14:21423790:G:C rs2013109 8.60 × 10−12 RNASE2 Intron WDF baseline MO CV SFL 1,651 –
14:55654183:T:C rs2094103 1.01 × 10−8 DLGAP5 Intron PLT-F ciprofloxacin 22 h PLT-F SD FSC 1,399 –
15:80260872:G:A rs67760360 6.95 × 10−21 BCL2A1 Regulatory, intron WDF LPS 18 h NE4 CV SFL 1,430 WBCb
20:4157072:C:G rs6084653 3.94 × 10−10 SMOX Intron RET baseline RET2 CV SFL 1,605 RBCb
20:57569860:C:G rs1043219 4.09 × 10−10 NELFCD Downstream, 3′UTR RET colchicine 20 h PLT CV SFL 1,334 PLTb
20:57597970:A:C rs463312 1.19 × 10−19 TUBB1 Missense, downstream PLT-F baseline IPF SD SFL 1,681 PLTb

Associations for blood traits and perturbation conditions were clumped to produce unique genomic regions across multiple conditions. Two-sided P values are based on t tests in linear regression models and are not adjusted for multiple testing. Variants with the lowest P value for each clumped region were selected as lead SNPs. The trait names contain the channel, condition and readout; for example, WDF Empa 1.5 h NE3 CV SFL indicates a readout in the WDF channel, with empagliflozin treatment, quantifying the SFL CV of a neutrophil subpopulation (NE3). This table contains a subset of regions with nearby candidate genes (see Supplementary Data 1 for a complete listing of associations). CV, coefficient of variation.

aThe previous association identified in ref. 17, which analyzed over 560,000 individuals.

bThe previous association identified in ref. 16, which analyzed over 173,000 individuals.