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. 2022 Oct 19;13:6204. doi: 10.1038/s41467-022-33906-5

Table 1.

Results summary of GWAS for microbial features

ID Chr Position rsID Effect allele EAF Other allele Microenv. Feature N (total) Beta ± s.e. P value Genes
1 2 17323400 rs1396075 T 0.76 A Moist c.Gammaproteobacteria 563 0.37 ± 0.067 3.4×10−08 ■
2 2 43812831 rs12466030 A 0.66 G Moist a.ASV070 [Veillonella (unc.)] 226 0.583 ± 0.103 1.7×10-08 THADA
3 3 9164097 rs2664121 T 0.73 G Dry g.Micrococcus 402 −0.33 ± 0.112 4.3×10-09 ENSG00000269886,SRGAP3
4 3 12514124 rs709165 G 0.54 A Moist a.ASV006 [S. hominis] 398 0.379 ± 0.069 4.0×10-08 MKRN2,MKRN2OS,RAF1,RNA5SP123,TSEN2
5 4 3266916 rs2159173 A 0.93 T Sebaceous a.ASV093 [Staphylococcus (unc.)] 276 −0.957 ± 0.159 1.8×10-09 HTT,MSANTD1,RGS12
6 4 55057749 rs55702239 G 0.77 A Dry o.Bacteroidales,g.Bacteroides 349 −0.43 ± 0.103 3.5×10-08 FIP1L1,PDGFRA
7 5 14584609 rs152620 A 0.79 T Moist g.Acinetobacter 454 −0.444 ± 0.081 3.7×10-08 OTULINL
8 6 69060156 rs9445997 T 0.62 C Sebaceous g.Staphylococcus 569 −0.328 ± 0.06 4.0×10-08 ■
9 6 93109029 rs2757026 C 0.51 T Moist f.Clostridiales_Incertae_Sedis_XI 363 −0.404 ± 0.072 2.2×10-08 ■
10 6 144022040 rs9484795 T 0.77 C Dry g.Anaerococcus 352 −0.41 ± 0.132 3.4×10-08 PHACTR2
11 7 57369680 rs11762959 A 0.55 G Moist o.Lactobacillales 489 0.348 ± 0.064 4.5×10-08 ■
12 7 57369974 rs7791487 A 0.56 T Moist f.Streptococcaceae 458 0.378 ± 0.064 3.4×10-09 ■
13 8 125763112 rs59379063 T 0.92 A Sebaceous a.ASV093 [Staphylococcus (unc.)] 279 −0.733 ± 0.133 3.2×10-08 ■
14 9 126919126 rs10121400 T 0.64 A Moist o.Burkholderiales 509 −0.354 ± 0.063 2.4×10-08 ■
15 11 106233170 rs17105612 G 0.94 A Moist a.ASV013 [S. epidermidis] 361 −0.928 ± 0.165 1.8×10-08 ■
16 12 96938142 rs12423627 T 0.93 C Sebaceous a.ASV002 [Staphylococcus (unc.)] 568 0.653 ± 0.113 6.9×10-09 CFAP54
17 12 101194600 rs4764996 G 0.93 A Dry a.ASV013 [S. epidermidis] 348 −1.2 ± 0.204 2.1×10-08 ANO4
18 13 33581388 rs1543797 T 0.75 C Dry Beta-diversity 511 ■ 3.2×10-08 ■
19 13 38067575 rs12583353 A 0.89 G Dry g.Paracoccus 372 −0.94 ± 0.144 5.6×10-10 ■
20 14 33629140 rs17100281 G 0.94 A Moist a.ASV021 [Micrococcus (unc.)] 331 −0.969 ± 0.176 3.7×10-08 NPAS3
21 16 28056516 rs8049083 C 0.72 A Sebaceous a.ASV004 [Corynebacterium (unc.)] 505 −0.378 ± 0.068 2.8×10-08 GSG1L
22 17 5341050 rs2472614 G 0.89 C Dry a.ASV086 [A. johnsonii] 255 −1.08 ± 0.186 4.7×10-08 C1QBP,DERL2,DHX33,ENSG00000263272,MIS12,NUP88,RABEP1,RPAIN
23 19 48742067 rs6509364 C 0.65 T Moist f.Rhodobacteraceae 377 −0.415 ± 0.072 8.5×10-09 CARD8,TMEM143,ZNF114

Single variant association tests were performed for each sample type and each microbial feature. Tests were adjusted for age, sex, body mass index (BMI) and genetic background (first ten genetic principal components). Positions are given as in genome assembly hg19 (GRCh37). Effect allele frequency (EAF) and total sample number (N) for the meta-analysis (sample pairs for dry) are shown. Results from moist and sebaceous skin sites were combined by meta-analysis (using METAL software for beta diversity and METASOFT software for univariate microbial features) and considered significant when PMeta value were genome-wide significant (PMeta < 5 × 10−8) and data sets were nominal significant (P < 0.05). Loci from dry data sets were considered significant when at least one data set resulted in genome-wide significance (lowest P value shown as PMeta) and the other in nominal significance. Meta-analyses were weighted by sample size for multivariate microbial feature and by inverse variance for univariate features. Effect sizes (β) and its standard error (s.e.) from meta-analyses are shown for moist and sebaceous. Effect size and standard error from tests with volar forearm are shown for dry skin. Tests were two-sided. Candidate causal variants were identified by fine-mapping or based on LD > 0.6 to the lead genetic variant. Genes with variants within their region (no formatted font) or with variants associated with their expression (italic font) are shown. Genes are shown in bold font when both conditions are met. Microbial features are prefixed with their level, amplicon variant sequence (a.), genus (g.), family (f.), order (o.), class (c.) or phylum (p.). Association with rs55702239 in dry sites have been identified with the non-redundant features o.Bacteroidales and g.Bacteroides. For simplicity, only statistics related to the genus level is shown in this case. ENSG00000263272 is a novel transcript, antisense to RPAIN and ENSG00000269886 is a novel transcript, antisense to TTLL3.