Identification of Susceptibility Genes for Peritoneal, Ovarian, and Deep Infiltrating Endometriosis Using a Pooled Sample-Based Genome-Wide Association Study

Table 1

Top ranked SNPs significantly associated with at least two endometriosis subtypes. Gene name is provided if the genotyped SNP is located in upstream, 3′UTR, intronic, exonic, 5′UTR, or downstream regions of that gene as annotated by Ensembl Genome Browser GRCh37 (Feb 2009). Inter denotes that a SNP is located in an intergenic region. Chr: chromosome. CV: coefficient of variation. In bold are figured the SNPs common to at least two endometriosis subtypes. Induction ratio is the ratio of gene expression in the endometriotic lesion as compared to the expression in the eutopic endometrium (data from Borghese, 2008). A ratio above 2.0 denotes an upregulation of the gene expression. A ratio below 0.50 denotes a downregulation of the gene expression.

SNP	Chr	SUP			OMA			DIE			Gene (induction ratio)
		Mean	CV	value	Mean	CV	value	Mean	CV	value
rs10754006	1	111,201	0,064	0,010	195,629	0,302	0,038				RGS1 (2.40) RGS18 (1.0)
rs776108	3	279,764	0,137	0,003	200,537	0,258	0,035	264,901	0,201	0,016	ROBO2 (1.58)
rs2035669	3	223,191	0,339	0,029				153,997	0,256	0,043	GPR156
rs2200224	4				0,008	0,156	0,026	0,008	0,162	0,027	SCFD2 (1.09) RASL11B (2.21)
rs6850850	4				71,599	0,064	0,013	176,564	0,292	0,047	TMEM33 (0.49)
rs343862	4	48,149	0,031	0,013				123,633	0,162	0,031	ARHGAP24
rs17089182	4	0,015	0,068	0,023	0,016	0,054	0,016				Inter
rs247004	5				131,934	0,142	0,017	156,523	0,148	0,012	ACSL6 (1.18)
rs4703908	5				116,523	0,153	0,029	107,713	0,184	0,047	ZNF366 (1.29)
rs17080695	5	73,986	0,124	0,049	45,071	0,050	0,021				MGAT1 (1.08)
rs17056959	6				0,015	0,106	0,044	0,014	0,078	0,024	GPR63 (2.69)
rs988147	6	413,289	0,314	0,005				319,292	0,341	0,020	SUPT3H
rs227849	6	321,093	0,325	0,016	333,485	0,289	0,016				RUNX2 (0.92) SUPT3H (1.20) CDC5L (1.31)
rs6946871	7				172,041	0,165	0,014	173,995	0,354	0,046	SDK1 (0.22)
rs17138951	7	0,004	0,422	0,030	0,005	0,416	0,038				ZNF680 (1.03)
rs6558435	8	236,327	0,468	0,041	181,398	0,150	0,011				ERICH1 (0.93) DLGAP2 (0.89)
rs10733833	10	136,688	0,205	0,033				176,217	0,269	0,027	CTNNA3, LRRTM3
rs6589535	11	132,232	0,277	0,042	78,770	0,133	0,035				Inter
rs10430848	11	254,632	0,439	0,028	148,169	0,187	0,026				TMEM16C (0.69)
rs2252178	12	194,081	0,413	0,035	168,457	0,333	0,044				Inter
rs1548094	14	0,009	0,187	0,023	0,010	0,182	0,024				Inter
rs11865033	16				0,043	0,025	0,009	0,044	0,012	0,000	MAF (1.79)
rs11647011	16	384,064	0,183	0,003	323,569	0,196	0,000				CLEC16A (0.78)
rs322609	16	74,431	0,004	0,000	110,368	0,343	0,042				CDH11 (1.70)
rs16949415	16	0,015	0,099	0,019	0,020	0,098	0,021				WWOX (1.88)
rs2472694	17	82,014	0,159	0,030	81,709	0,223	0,035				GRAP (1.35) PRPSAP2 (0.73) SLC5A10 (1.36)
rs10871642	18				54,143	0,111	0,038	50,092	0,108	0,039	CCDC102B (1.83)
rs3746192	19	93,400	0,173	0,006	78,952	0,149	0,009	97,912	0,063	0,000	KCNN1 (1.02)
rs6049295	20	137,490	0,198	0,007				90,072	0,146	0,015	Inter
rs1884779	20	141,503	0,362	0,031	118,669	0,360	0,035				SULF2 (1.42)
rs7291901	22				0,091	0,030	0,032	0,078	0,029	0,022	XPNPEP3 (0.49)
rs16986515	X	113,443	0,037	0,000				248,589	0,543	0,020	AMELX, ARHGAP6, MSL3L1