Chapter22

Case	Control
497	459709

Case

Control

497

459709

Top SNP Information

Location	SNP	Gene	Ref>Alt	Alt in Case	Alt in Control	Chi-square	P-value	Odds Ratio
chr4:177863637	rs2728145	-	C>T	65	28287	36.28	1.705e-09	2.124
chr10:34339539	rs16935028	-	G>T	45	18629	28.69	8.496e-08	2.216
chr4:177849348	rs1436190	-	G>A	142	83748	27.31	1.737e-07	1.595
chr10:135060539	rs1984262	-	G>A	71	34800	27.27	1.772e-07	1.88
chr4:177863886	rs2574926	-	T>C	60	28269	26.78	2.278e-07	1.965
chr10:34334898	rs10508795	-	C>T	45	19063	26.76	2.299e-07	2.159
chr18:73278094	rs41512245	-	C>T	35	13601	26.13	3.19e-07	2.347
chr21:45716135	rs28408186	AIRE	G>A	42	17610	25.91	3.575e-07	2.186
chr5:173754762	rs2964096	-	T>C	102	56041	25.47	4.495e-07	1.682
chr7:14292413	rs77071667	DGKB	G>A	46	20054	25.21	5.148e-07	2.096
chr5:80449200	rs76360570	RASGRF2	T>C	31	11660	24.91	6.011e-07	2.415
chr4:177862976	rs2728147	-	G>T	58	27689	24.64	6.905e-07	1.932
chr5:89576758	rs2943029	-	G>T	48	21351	24.62	6.991e-07	2.05
chr10:135195332	rs2185746	PAOX	G>A	98	54313	24.1	9.141e-07	1.673
chr2:12461724	rs74329373	-	C>T	33	13151	23.01	1.61e-06	2.283
chr8:82044456	rs79232062	-	G>A	27	9978	22.7	1.892e-06	2.46
chr10:135103315	rs113340564	TUBGCP2	C>T	125	74481	22.58	2.014e-06	1.566
chr20:38703982	rs78744070	-	G>T	222	150535	22.46	2.147e-06	1.43
chr19:8792566	rs2340549	-	A>G	386	281799	21.94	2.813e-06	1.345
chr17:32347617	rs78426036	ASIC2	G>A	37	15724	21.65	3.271e-06	2.14
chr4:177863637	rs2728145	-	C>T	33	12577	28.17	1.109e-07	2.483
chr7:29434042	rs60152274	AC004593.2	C>T	95	52005	28.08	1.165e-07	1.759
chr10:135195332	rs2185746	PAOX	G>A	83	44996	25.53	4.346e-07	1.772
chr23:122338993	rs150326109	GRIA3	C>G	41	18804	25.18	5.218e-07	2.197
chr2:12461724	rs74329373	-	C>T	31	12136	24.71	6.669e-07	2.41
chr5:173754762	rs2964096	-	T>C	87	48228	24.17	8.827e-07	1.727
chr20:35056903	rs75758696	DLGAP4	G>A	47	21786	23.81	1.064e-06	2.043
chr20:38703982	rs78744070	-	G>T	190	130475	22.26	2.378e-06	1.464
chr5:149237916	rs30884	PDE6A	C>T	499	396090	21.2	4.147e-06	1.34
chr2:15904041	rs2544531	-	G>A	548	441262	20.98	4.641e-06	1.34
chr4:177862976	rs2728147	-	G>T	30	12374	20.84	4.981e-06	2.279
chr2:15913628	rs34092493	-	CA>C	555	447958	20.64	5.535e-06	1.337
chr14:49708666	rs117473478	-	C>T	63	34828	20.63	5.574e-06	1.797
chr8:132359916	rs4446719	-	C>T	21	7549	20.38	6.356e-06	2.611
chr20:38741745	rs4810289	-	C>T	147	95973	20.11	7.311e-06	1.489
chr19:8792566	rs2340549	-	A>G	340	255764	20.08	7.425e-06	1.349
chr7:27230831	rs17427917	-	T>C	53	27006	19.89	8.211e-06	1.859
chr16:8520158	rs12934978	-	C>T	311	231424	19.83	8.449e-06	1.355
chr2:15912926	rs10929387	-	G>A	552	445669	19.59	9.602e-06	1.325
chr10:135175844	rs11101707	-	C>T	78	44533	19.5	1.004e-05	1.675

Associated Phenotypes ^ⓘ

Name

Top Correlation

ID	Name	Top Correlation
HP: 0000118	Phenotypic abnormality	0/20
HP: 0000707	Abnormality of the nervous system	0/20
HP: 0000765	Abnormality of the thorax	0/20
HP: 0000772	Abnormality of the ribs	0/20
HP: 0000924	Abnormality of the skeletal system	0/20
HP: 0000951	Abnormality of the skin	0/20
HP: 0001155	Abnormality of the hand	0/20
HP: 0001167	Abnormality of finger	0/20
HP: 0001547	Abnormality of the rib cage	0/20
HP: 0001574	Abnormality of the integument	0/20
HP: 0001939	Abnormality of metabolism/homeostasis	0/20
HP: 0002011	Morphological central nervous system abnormality	0/20
HP: 0002086	Abnormality of the respiratory system	0/20
HP: 0002664	Neoplasm	0/20
HP: 0002715	Abnormality of the immune system	0/20
HP: 0002795	Functional respiratory abnormality	0/20
HP: 0002813	Abnormality of limb bone morphology	0/20
HP: 0002817	Abnormality of the upper limb	0/20
HP: 0002890	Thyroid carcinoma	0/20
HP: 0003006	Neuroblastoma	0/20
HP: 0004375	Neoplasm of the nervous system	0/20
HP: 0004376	Neuroblastic tumor	0/20
HP: 0005368	Abnormality of humoral immunity	0/20
HP: 0005372	Abnormality of B cell physiology	0/20
HP: 0006742	Congenital neuroblastoma	0/20
HP: 0009121	Abnormal axial skeleton morphology	0/20
HP: 0010561	Undulate ribs	0/20
HP: 0010701	Abnormal immunoglobulin level	0/20
HP: 0010702	Increased antibody level in blood	0/20
HP: 0010978	Abnormality of immune system physiology	0/20
HP: 0011017	Abnormal cellular physiology	0/20
HP: 0011121	Abnormality of skin morphology	0/20
HP: 0011297	Abnormal digit morphology	0/20
HP: 0011314	Abnormality of long bone morphology	0/20
HP: 0011355	Localized skin lesion	0/20
HP: 0011772	Abnormality of thyroid morphology	0/20
HP: 0011779	Anaplastic thyroid carcinoma	0/20
HP: 0011792	Neoplasm by histology	0/20
HP: 0011793	Neoplasm by anatomical site	0/20
HP: 0011842	Abnormality of skeletal morphology	0/20
HP: 0011844	Abnormal appendicular skeleton morphology	0/20
HP: 0012379	Abnormal enzyme/coenzyme activity	0/20
HP: 0012517	Reduced catalase activity	0/20
HP: 0012639	Abnormal nervous system morphology	0/20
HP: 0025131	Finger swelling	0/20
HP: 0025354	Abnormal cellular phenotype	0/20
HP: 0030060	Nervous tissue neoplasm	0/20
HP: 0030061	Neuroectodermal neoplasm	0/20
HP: 0030063	Neuroepithelial neoplasm	0/20
HP: 0030065	Primitive neuroectodermal tumor	0/20
HP: 0030067	Peripheral primitive neuroectodermal neoplasm	0/20
HP: 0030878	Abnormality on pulmonary function testing	0/20
HP: 0031071	Abnormal endocrine morphology	0/20
HP: 0031409	Abnormal lymphocyte physiology	0/20
HP: 0040064	Abnormality of limbs	0/20
HP: 0040068	Abnormality of limb bone	0/20
HP: 0045049	Abnormal DLCO	0/20
HP: 0045051	Decreased DLCO	0/20
HP: 0100006	Neoplasm of the central nervous system	0/20
HP: 0100031	Neoplasm of the thyroid gland	0/20
HP: 0100568	Neoplasm of the endocrine system	0/20
HP: 0100836	Malignant neoplasm of the central nervous system	0/20
HP: 0200041	Skin erosion	0/20
HP: 0410244	Abnormal IgD level	0/20
HP: 0410246	Increased circulating IgD level	0/20

Name

Top Correlation

HP: 0000118

Phenotypic abnormality

0/20

HP: 0000707

Abnormality of the nervous system

0/20

HP: 0000765

Abnormality of the thorax

0/20

HP: 0000772