Table 2 Genome-wide significant SNPs associated with the microbiota parameters.

Bacterial group/diversity index	Sample	Locus	SNP	Chr	Position^a	Minor/major allele	MAF^b	Effect size (SE)^c	The proportion of variance explained	P-value	Protein expression level in the small intestine (glandular cells)^f	Protein expression level in the colon (endothelial cells)^f	Protein expression level in the colon (glandular cells)^f	Protein expression level in the colon (peripheral nerve/ganglion)^f
Relative abundance
Prevotella	Male	2p16.1	rs6545786	2	60403018	T/C	0.23	2.015 (0.366)	0.018	5.93E−08
Faecalibacterium	Male	HS3ST4	rs3803713	16	25838494	T/C	0.15	0.111 (0.020)	0.013	8.29E−08
Oscillospira	Female	10p15.1	rs1033781	10	4331114	G/T	0.14	−0.047 (0.008)	0.011	5.28E−08
Erysipelotrichaceae;g	Female	C2CD2	rs2839417	21	43319737	G/A	0.28	0.250 (0.045)	0.020	5.96E−08	++	+	++	++
Alpha diversity index
Chao1	Female	18q12.2	rs885034	18	36001573	C/A	0.15	78.19 (14.37)	0.012	8.24E−08

^aPositions were derived from dbSNP build 137.
^bThe minor allele frequency calculated using the data from all subjects.
^cLinear regression coefficient beta and standard error (SE) of the minor allele.
^dThe proportion of variance explained by individual SNPs calculated based on the effect of a minor allele on the standardized trait
^eSNPs were annotated with SNPnexus (http://snp-nexus.org/index.html).
^fProtein expression levels of overlapped genes in intestinal and colonic tissues according to The Human Protein Atlas (http://www.proteinatlas.org/). +++: High, ++: Medium, +: Low, –: Not detected.
Chr chromosome, SNP single nucleotide polymorphism, MAF minor allele frequency.

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