Table 1.

Pathways with significant enrichment in the BCC GWAS.

Pathway1	Gene Count2	Genes with eSNP (%)	FDR3	Pathway Enrichment p-value	Genes with Pbcc < 0.014	eSNP5	eSNP Pbcc	Chr	Position	Distance (bp)
Autoimmune thyroid disease	55	25(45.5)	0.24	<0.001	HLA-B	rs3093562	1.21E-04	6	31659516	226,548
					HLA-G	rs805262	5.15E-04	6	31736712	1,829,834
					HLA-DQB1	rs2736171	7.53E-04	6	31703466	1,032,168
					HLA-DRB36	rs2856683	8.19E-04	6	32763196	97,656
					HLA-DRB1	rs7536479	1.92E-03	1	99838156	NA7
					HLA-DOB	rs10947342	1.92E-03	6	32828758	59,759
					IFNA14	rs9299397	4.09E-03	9	93514692	72,284,714
					HLA-DPA1	rs13215763	4.11E-03	6	33104578	36,193
					HLA-DRB4	rs7775228	4.72E-03	6	32766057	285,383
					HLA-C	rs2854050	5.10E-03	6	32293583	945,749
					HLA-A	rs9461216	5.38E-03	6	25916722	4,101,587
					HLA-DMA	rs2857211	5.54E-03	6	32848420	175,952
					HLA-DPB1	rs3130171	6.26E-03	6	33106707	45,030
					HLA-DOA	rs6920606	7.29E-03	6	33105652	20,285
JAK-STAT signaling pathway	155	60(38.7)	0.49	0.02	IL21R	rs4787976	2.93E-03	16	27513198	143,582
					STAM2	rs10930939	2.96E-03	2	152688179	6,619
					IFNA14	rs9299397	4.09E-03	9	93514692	72,284,714
					IL15RA	rs8177600	7.43E-03	10	6065069	4,921
					CSF2RB	rs2284027	9.25E-03	22	35595025	44,595
					IL6ST	rs17730330	9.47E-03	12	91522645	NA7
					PIK3CB	rs6439828	9.68E-03	3	140113284	152,409

¹Pathways are from the Kyoto Encyclopedia of Genes and Genomes (KEGG)

²The number of genes in the pathway according to the KEGG database

³Based on 1000 permutations and 99 tested pathway in total

⁴P_BCC represents p values of eSNPs for BCC association. Only the genes whose representative eSNPs reached P_BCC < 0.01 are listed here and the information of all enriched genes in the two pathways are listed in Table S2

⁵Denotes genes with the smallest P_BCC

⁶The four genes HLA-DRB3, HLA-DRB5, HLA-DQA1, and HLA-DQA2 have the same representative eSNP: rs2856683

⁷This is a trans eQTL. The eSNP is not on the same chromosome as the associated gene.