Runs of homozygosity and inbreeding in thyroid cancer

Thomsen, Hauke; Chen, Bowang; Figlioli, Gisella; Elisei, Rossella; Romei, Cristina; Cipollini, Monica; Cristaudo, Alfonso; Bambi, Franco; Hoffmann, Per; Herms, Stefan; Landi, Stefano; Hemminki, Kari; Gemignani, Federica; Försti, Asta

doi:10.1186/s12885-016-2264-7

BMC Cancer

Table 1 Association between homozygosity and susceptibility to TC for individual SNPs

From: Runs of homozygosity and inbreeding in thyroid cancer

SNP	CHR	BP^a	Cases AA/BB	Cases AB	Controls AA/BB	Controls AB	chi²	P ^b	q ^*c	Genes
rs4698482	4	16020011	519	116	274	157	44.43	2.62 × 10⁻¹¹	1.40 × 10⁻⁵	LDB2
rs11688848	2	204624451	512	119	275	156	40.10	2.40 × 10⁻¹⁰	5.38 × 10⁻⁵	ICOS
rs9578483	13	22068754	543	97	296	135	39.66	3.01 × 10⁻¹⁰	5.38 × 10⁻⁵	FGF9, FTHL7
rs839509	2	212530542	497	126	270	160	37.09	1.12 × 10⁻⁹	0.0001	ERBB4, CPS1, hCG_1645016
rs2414003	15	48105489	514	122	280	151	33.90	5.77 × 10⁻⁹	0.0006	ATP8B4, SLC27A2
rs3096381	16	69875502	525	116	289	141	30.46	3.39 × 10⁻⁸	0.0028	FLJ11171, HYDIN, CALB2
rs630695	6	117359452	526	103	299	132	30.10	4.09 × 10⁻⁸	0.0028	RFXDC1, GPRC6A, VGLL2
rs938845	18	63860975	512	122	284	147	30.02	4.26 × 10⁻⁸	0.0028	NA
rs17797954	5	174303096	516	122	287	144	28.09	1.15 × 10⁻⁷	0.0068	DRD1
rs10961997	9	15361675	509	134	279	152	27.48	1.58 × 10⁻⁷	0.0083	SNAPC3
rs12126497	1	166939482	586	56	346	85	27.33	1.71 × 10⁻⁷	0.0083	DPT, XCL1
rs509716	6	131475408	532	113	297	134	26.90	2.13 × 10⁻⁷	0.0095	EPB41L2, AKAP7
rs6715968	2	229884476	484	141	272	159	25.75	3.86 × 10⁻⁷	0.0159	PID1, DNER
rs712082	1	222792683	545	98	311	120	25.32	4.83 × 10⁻⁷	0.0173	WDR26, AKR1B1P1
rs6440553	3	149713261	545	84	321	110	25.32	4.84 × 10⁻⁷	0.0173	RPL38P1
rs8043171	15	90065471	529	105	304	127	25.07	5.50 × 10⁻⁷	0.0184	SLCO3A1
rs12902263	15	69429108	556	87	321	110	24.77	6.44 × 10⁻⁷	0.0197	THSD4, hCG_2004593, NR2E3
rs10254361	7	119351441	522	116	296	135	24.72	6.62 × 10⁻⁷	0.0197	KCND2
rs11563992	7	27347461	507	115	294	136	24.16	8.86 × 10⁻⁷	0.0242	NA
rs7018634	9	20249528	538	100	310	121	24.11	9.05 × 10⁻⁷	0.0242	SLC24A2, SMNP
rs11169076	12	48261675	571	72	335	96	23.99	9.68 × 10⁻⁷	0.0247	MCRS1, FAM186B
rs1943939	18	69856260	556	62	342	89	23.22	1.43 × 10⁻⁶	0.0332	FBXO15,
rs12660310	6	167051901	503	120	292	139	23.18	1.46 × 10⁻⁶	0.0332	RPS6KA2, RNASET2
rs11204947	1	150484881	489	135	280	151	23.16	1.48 × 10⁻⁶	0.0332	HRNR, FLG,
rs3821310	2	74923771	581	61	345	85	23.06	1.56 × 10⁻⁶	0.0335	HK2, SEMA4F, POLE4
rs9407406	9	8229748	532	95	314	117	22.93	1.67 × 10⁻⁶	0.0345	C9orf123, PTPRD
rs2830028	21	26349119	493	133	282	148	22.64	1.94 × 10⁻⁶	0.0386	APP, GABPA, CYYR1
rs11151652	18	67133203	554	91	319	110	22.52	2.07 × 10⁻⁶	0.0397	CBLN2
rs10779770	1	12529312	537	97	314	117	22.42	2.18 × 10⁻⁶	0.0403	VPS13D, DHRS3
rs1508833	5	38050010	519	108	303	127	22.35	2.26 × 10⁻⁶	0.0404	GDNF, EGFLAM
rs554232	8	102533760	540	98	314	117	22.23	2.40 × 10⁻⁶	0.0408	NACAP1, GRHL2
rs2102727	8	53063166	502	133	285	146	22.21	2.43 × 10⁻⁶	0.0408	PCMTD1, ST18,
rs9379246	6	8777273	571	67	341	90	22.11	2.56 × 10⁻⁶	0.0416	HULC
rs7481683	11	8157762	454	174	252	179	21.98	2.75 × 10⁻⁶	0.0434	RIC3, LMO1

^aGenome build hg18
^b P was calculated using a simple 2x2 chi² test based on the number of homozygotes and heterozygotes at each SNP in cases and controls
^c q ^*values representing the false discovery rate (FDR)

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