Skip to main content

Table 1 Characteristics of selected SNPs for core gut microbiota

From: Assessment of bidirectional relationships between 98 genera of the human gut microbiota and amyotrophic lateral sclerosis: a 2-sample Mendelian randomization study

Core gut microbiota SNP Chr. Locus start Locus end A1 A2 P Beta SE β-div P Nearest gene Genes in locus Variance explained
OTU10032 unclassifed Enterobacteriaceae Species-level OTU rs1009634 12 4,779,313 4,900,344 G A 7.12E-09 −1.3 0.23 0.93 AKAP3 NDUFA9, GALNT8, RP11-234B24.2 0.0183
Bacilli class rs10928827 2 129,426,740 129,473,850 G A 1.02E-08 −0.2 0.04 0.19 HS6ST1 0.0180
Lactobacillales order rs10928827 2 129,426,740 129,473,850 G A 4.19E-09 −0.2 0.04 0.19 HS6ST2 0.0189
Unclassifed Erysipelotrichaceae rs11626933 14 90,681,816 90,810,659 G A 1.83E-08 −0.2 0.04 0.55 C14orf102 C14orf102 0.0173
Marinilabiliaceae family rs11724031 4 77,441,448 77,467,405 G A 2.44E−10 −1 0.15 0.68 SHROOM3 SHROOM3 0.0219
Unclassifed Marinilabiliaceae rs11724031 4 77,441,448 77,467,405 G A 2.44E-10 -1 0.15 0.68 SHROOM3 SHROOM3 0.0219
Erysipelotrichaceae family rs11877825 18 10,566,345 10,595,758 G T 2.82E-11 −0.3 0.04 0.34 NAPG 0.0242
Erysipelotrichia class rs11877825 18 10,566,345 10,595,758 G T 2.82E-11 −0.3 0.04 0.34 NAPG 0.0242
Erysipelotrichales order rs11877825 18 10,566,345 10,595,758 G T 2.82E-11 −0.3 0.04 0.34 NAPG 0.0242
Marinilabiliaceae family rs11915634 3 1,452,602 1,517,331 T C 2.99E-10 −1.3 0.21 0.14 CNTN6 0.0217
Unclassifed Marinilabiliaceae rs11915634 3 1,452,602 1,517,331 T C 2.99E-10 −1.3 0.21 0.14 CNTN7 0.0217
OTU10032 unclassifed Enterobacteriaceae rs12149695 16 27,205,994 27,293,886 A T 1.82E-09 0.61 0.10 0.23 FLJ21408 NSMCE1, FLJ21408, KDM8 0.0198
OTU15355 Dialister Species-level OTU rs12442649 15 37,968,393 38,035,538 G A 3.72E-08 −1.5 0.27 0.85 TMCO5A 0.0166
EscherichiaShigella rs13096731 3 58,014,818 58,089,851 A G 2.55E-08 −0.4 0.08 0.12 FLNB FLNB 0.0170
OTU10032 unclassifed Enterobacteriaceae rs13276516 8 56,589,428 56,596,140 A G 5.54E-09 − 0.6 0.10 0.41 TGS1 0.0186
Lactobacillales order rs1362404 16 51,955,443 52,017,380 T G 1.56E-08 0.23 0.04 7.50E-05 TOX3 0.0175
Bacilli class rs148330122 19 38,497,288 38,631,252 C T 1.32E-09 −0.5 0.08 0.18 SIPA1L3 SIPA1L3 0.0201
OTU10032 unclassifed Enterobacteriaceae rs17085775 9 71,165,704 71,167,878 C T 2.06E-08 −1 0.18 0.54 C9orf71 0.0172
Erysipelotrichaceae family rs17421787 4 131,293,675 131,512,291 C G 3.60E-08 −0.3 0.05 0.16 RP11-22 J15.1 0.0166
Erysipelotrichales order rs17421787 4 131,293,675 131,512,291 C G 3.60E-08 −0.3 0.05 0.16 RP11-22 J15.2 0.0166
Erysipelotrichia class rs17421787 4 131,293,675 131,512,291 C G 3.60E-08 −0.3 0.05 0.16 RP11-22 J15.3 0.0166
Unclassifed Acidaminococcaceae rs17661843 7 48,381,902 48,433,594 T C 3.72E-14 −1.4 0.18 0.26 ABCA13 ABCA13 0.0312
Bacilli class rs2071199 20 43,030,809 43,037,422 T C 1.24E-08 −0.3 0.06 0.58 HNF4A–AS1 HNF4A 0.0178
OTU10032 unclassifed Enterobacteriaceae Species-level OTU rs2318350 8 139,889,972 139,942,500 T C 3.65E-09 −1.2 0.19 0.95 COL22A1 COL22A1 0.0190
OTU10032 unclassifed Enterobacteriaceae rs249733 5 141,877,862 141,911,748 T C 4.74E-10 −0.7 0.10 0.68 SPRY4 0.0212
Actinobacteria class rs34613612 21 32,184,901 32,204,347 C G 6.34E-10 0.25 0.04 9.87E-03 KRTAP8–1 KRTAP8–1 0.0209
Actinobacteria phylum rs34613612 21 32,184,901 32,204,347 C G 6.34E-10 0.25 0.04 9.87E-03 KRTAP8–1 KRTAP8–1 0.0209
Enterobacteriaceae family rs35275482 15 60,027,987 60,128,040 C A 3.72E-11 −0.5 0.08 0.06 BNIP2 0.0239
Enterobacteriales order rs35275482 15 60,027,987 60,128,040 C A 3.72E-11 −0.5 0.08 0.06 BNIP3 0.0239
OTU10032 unclassifed Enterobacteriaceae Species-level OTU rs3925158 3 38,161,078 38,313,688 C G 6.29E-09 −1 0.17 0.78 SLC22A13 SLC22A13, MYD88, DLEC1, ACAA1, OXSR1 0.0185
Gammaproteobacteria class rs4621152 2 217,857,450 217,924,261 C T 1.40E-08 −0.3 0.05 0.79 AC007557.1 0.0176
Blautia genus rs4669413 2 9,801,744 9,818,596 T C 1.20E-08 −0.2 0.03 0.75 RP11–521D12.1 0.0178
Bacilli class rs479105 12 3,357,596 3,393,503 T C 1.21E-08 −0.2 0.04 0.48 PRMT8 0.0178
Unclassifed Acidaminococcaceae rs56006724 2 228,486,044 228,523,585 A G 6.35E-10 −0.9 0.14 0.93 C2orf83 C2orf83 0.0209
Lactobacillales order rs59042687 3 95,359,287 95,823,523 T G 6.22E-09 −0.2 0.04 0.02 LINC00879 0.0185
OTU13305 Fecalibacterium Species-level OTU rs597205 1 112,379,026 112,415,622 T C 7.68E-09 −0.6 0.11 0.85 C1orf183 C1orf183 0.0183
Lactobacillales order rs62295801 3 162,444,724 163,236,170 G T 5.32E-10 −0.3 0.04 0.21 LINC01192 LINC01192 0.0211
Lactobacillales order rs7083345 10 7,020,329 7,044,987 T C 2.89E-09 0.24 0.04 0.02 RP11-554I8.2 0.0199
Bacilli class rs7083345 10 7,020,329 7,044,987 T C 3.38E-10 0.25 0.04 0.02 RP11-554I8.2 0.0209
Lactobacillales order rs7113056 11 122,091,502 122,154,110 C T 1.72E-13 −0.5 0.07 0.07 RP11-166D19.1 0.0296
Unclassifed Acidaminococcaceae rs75036654 1 37,717,219 37,780,821 C T 4.94E-10 −1.4 0.22 0.06 LINC01137 0.0212
Bacilli class rs7646786 3 185,729,634 185,742,372 T C 2.29E-08 −0.2 0.04 0.5 LOC344887 0.0171
Unclassifed Porphyromonadaceae rs7656342 4 9,721,358 9,895,176 A G 2.80E-09 0.39 0.07 0.22 DRD5 SLC2A9, DRD5 0.0193
Blautia genus rs79387448 2 103,099,953 103,239,356 C T 7.68E-11 −0.3 0.05 0.66 SLC9A2 SLC9A2 0.0231
Unclassifed Porphyromonadaceae rs9291879 5 66,515,817 66,550,855 C T 3.51E-09 −0.6 0.10 0.08 CD180 0.0191
Gammaproteobacteria class rs9300430 13 98,269,478 98,306,405 C T 1.30E-09 −0.6 0.10 0.12 RAP2A 0.0201
Proteobacteria phylum rs9323326 14 58,476,448 58,532,709 A G 8.76E-10 −0.2 0.03 0.02 SLC35F4 C14orf37 0.0206
Unclassifed Enterobacteriaceae rs938295 1 16,087,164 16,124,985 C T 2.34E-08 −0.5 0.09 0.76 FBLIM1 FBLIM1 0.0171
Unclassifed Marinilabiliaceae rs9831278 3 98,879,786 98,942,990 C T 2.53E-08 −1.2 0.21 0.49 LINC00973 0.0170
Marinilabiliaceae family rs9831278 3 98,879,786 98,942,990 C T 2.53E-08 −1.2 0.21 0.49 LINC00974 0.0170
Unclassifed Acidaminococcaceae rs986417 14 60,787,269 61,122,040 C T 2.63E-09 −1.4 0.23 0.47 SIX6 SIX6, C14orf39, SIX1 0.0194
Marinilabiliaceae family rs9996716 4 77,441,448 77,467,405 G A 5.58E-09 −0.7 0.12 0.2 SHROOM3 SHROOM3 0.0186
Unclassifed Marinila-biliaceae rs9996716 4 77,441,448 77,467,405 G A 5.58E-09 −0.7 0.12 0.2 SHROOM3 SHROOM3 0.0186
  1. The 53 associations with bacterial abundance are grouped into 40 loci on the basis of LD. SNP single-nucleotide polymorphisms, Chr chromosome, A1 effect allele, A2 non-effect allele, P meta-analysis P value for A1, Beta meta-analysis coeffcient for A1, SE standard error, β-div P P value for association with β diversity.