Variant report

Variant	nsv1004458
Chromosome Location	chr3:301064-349419
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr3:305517-307368	HepG2	liver:	n/a	n/a
2	ATF2	chr3:319964-320748	GM12878	blood:	n/a	n/a
3	ATF2	chr3:331761-332103	GM12878	blood:	n/a	n/a
4	ATF2	chr3:319829-320847	GM12878	blood:	n/a	n/a
5	ATF3	chr3:306304-306760	A549	lung:	n/a	n/a
6	BATF	chr3:319906-320293	GM12878	blood:	n/a	n/a
7	BATF	chr3:320384-320805	GM12878	blood:	n/a	n/a
8	BATF	chr3:341729-341996	GM12878	blood:	n/a	n/a
9	BATF	chr3:319974-320310	GM12878	blood:	n/a	n/a
10	BCL11A	chr3:319942-320280	GM12878	blood:	n/a	chr3:320201-320210 chr3:320061-320069
11	BCL11A	chr3:319927-320341	GM12878	blood:	n/a	chr3:320201-320210 chr3:320061-320069
12	BCL3	chr3:320464-320727	GM12878	blood:	n/a	n/a
13	BCL3	chr3:306315-306750	A549	lung:	n/a	n/a
14	BCL3	chr3:306168-306863	A549	lung:	n/a	chr3:306285-306294 chr3:306282-306291
15	BCLAF1	chr3:320388-320763	GM12878	blood:	n/a	n/a
16	BHLHE40	chr3:319378-320826	GM12878	blood:	n/a	n/a
17	BHLHE40	chr3:342270-342502	GM12878	blood:	n/a	n/a
18	BHLHE40	chr3:306286-306823	HepG2	liver:	n/a	n/a
19	BRCA1	chr3:306367-306903	Hela-S3	cervix:	n/a	n/a
20	BRCA1	chr3:306406-306600	HepG2	liver:	n/a	n/a
21	CEBPB	chr3:306243-306864	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
22	CEBPB	chr3:306266-306559	MCF-7	breast:	n/a	chr3:306309-306322 chr3:306463-306480
23	CEBPB	chr3:306278-306814	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
24	CEBPB	chr3:302689-302981	Hela-S3	cervix:	n/a	chr3:302812-302825
25	CEBPB	chr3:306097-307016	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
26	CEBPB	chr3:306302-306792	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
27	CEBPB	chr3:306177-307012	Hela-S3	cervix:	n/a	chr3:306309-306322 chr3:306463-306480
28	CEBPB	chr3:306264-306872	IMR90	lung:	n/a	chr3:306309-306322 chr3:306463-306480
29	CEBPB	chr3:306264-306781	A549	lung:	n/a	chr3:306309-306322 chr3:306463-306480
30	CEBPB	chr3:306302-306622	MCF-7	breast:	n/a	chr3:306309-306322 chr3:306463-306480
31	CEBPB	chr3:306331-306724	HepG2	liver:	n/a	chr3:306463-306480
32	CEBPB	chr3:306282-306969	HepG2	liver:	n/a	chr3:306309-306322 chr3:306463-306480
33	CEBPB	chr3:320077-320362	HepG2	liver:	n/a	chr3:320218-320229
34	CEBPD	chr3:306328-306607	HepG2	liver:	n/a	n/a
35	CHD1	chr3:341448-341614	GM12878	blood:	n/a	n/a
36	CHD2	chr3:319756-320739	GM12878	blood:	n/a	n/a
37	CREB1	chr3:306269-306913	HepG2	liver:	n/a	n/a
38	CREB1	chr3:306373-306822	A549	lung:	n/a	n/a
39	CREB1	chr3:306196-306931	HepG2	liver:	n/a	n/a
40	CTCF	chr3:340160-340310	HUVEC	blood vessel:	n/a	n/a
41	CUX1	chr3:319594-320940	GM12878	blood:	n/a	n/a
42	CUX1	chr3:341633-342014	GM12878	blood:	n/a	n/a
43	E2F4	chr3:306302-306616	MCF10A-Er-Src	breast:	n/a	n/a
44	EBF1	chr3:331685-332343	GM12878	blood:	n/a	n/a
45	EBF1	chr3:319862-320350	GM12878	blood:	n/a	chr3:320133-320146 chr3:320135-320144 chr3:320135-320145 chr3:320134-320145
46	EBF1	chr3:312560-312707	GM12878	blood:	n/a	n/a
47	EBF1	chr3:319068-320868	GM12878	blood:	n/a	chr3:320133-320146 chr3:320135-320144 chr3:320135-320145 chr3:320134-320145
48	EBF1	chr3:319831-320407	GM12878	blood:	n/a	chr3:320133-320146 chr3:320135-320144 chr3:320135-320145 chr3:320134-320145
49	EBF1	chr3:322542-322796	GM12878	blood:	n/a	chr3:322704-322715
50	EBF1	chr3:341471-342010	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:347869-347919	NT2-D1	testis:	n/a
2	chr3:347869-347919	NT2-D1	testis:	n/a
3	chr3:347869-347919	SK-N-SH	brain:	n/a
4	chr3:347869-347919	RPTEC	kidney:	n/a
5	chr3:347869-347919	NHDF-neo	bronchial:	n/a
6	chr3:347869-347919	NB4	blood:	n/a
7	chr3:347869-347919	NHBE	bronchial:	n/a
8	chr3:347869-347919	A549	lung:	n/a
9	chr3:347869-347919	MCF-7	breast:	n/a
10	chr3:347869-347919	AG09319	gingival:	n/a
11	chr3:347869-347919	HCF	heart:	n/a
12	chr3:347869-347919	AG04449	skin:	fetal
13	chr3:347869-347919	HMEC	breast:	n/a
14	chr3:347869-347919	HL-60	blood:	n/a
15	chr3:347869-347919	GM06990	blood:	n/a
16	chr3:347869-347919	GM12891	blood:	n/a
17	chr3:347869-347919	GM12878	blood:	n/a
18	chr3:347869-347919	MCF10A-Er-Src	breast:	n/a
19	chr3:347869-347919	AG04450	lung:	fetal
20	chr3:347869-347919	BE2_C	brain:	n/a
21	chr3:347869-347919	ProgFib	skin:	n/a
22	chr3:347869-347919	AG09309	skin:	n/a
23	chr3:347869-347919	PrEC	prostate:	n/a
24	chr3:347869-347919	HRPEpiC	eye:	n/a
25	chr3:347869-347919	HCPEpiC	choroid plexus:	n/a
26	chr3:347869-347919	H1-hESC	embryonic stem cell:	embryo
27	chr3:347869-347919	NH-A	brain:	n/a
28	chr3:347869-347919	AG10803	skin:	n/a
29	chr3:347869-347919	PFSK-1	brain:	n/a
30	chr3:347869-347919	BJ	skin:	n/a
31	chr3:347869-347919	HEK293	kidney:	embryo
32	chr3:347869-347919	U87	brain:	n/a
33	chr3:347869-347919	SKMC	muscle:	n/a
34	chr3:347869-347919	Hepatocyte	liver:	n/a
35	chr3:347869-347919	HAEpiC	amniotic membrane:	n/a
36	chr3:347869-347919	HNPCEpiC	eye:	n/a
37	chr3:347869-347919	PANC-1	pancreas:	n/a
38	chr3:347869-347919	Jurkat	blood:	n/a
39	chr3:347869-347919	SK-N-SH_RA	brain:	n/a
40	chr3:347869-347919	AoSMC	blood vessel:	n/a
41	chr3:347869-347919	HEEpiC	esophagus:	n/a
42	chr3:347869-347919	K562	blood:	n/a
43	chr3:347869-347919	HCT-116	colon:	n/a
44	chr3:347869-347919	LNCaP	prostate:	n/a
45	chr3:347869-347919	GM19239	blood:	n/a
46	chr3:347869-347919	T-47D	breast:	n/a
47	chr3:347869-347919	SAEC	small airway:	n/a
48	chr3:347869-347919	HRCEpiC	kidney:	n/a
49	chr3:347869-347919	HUVEC	blood vessel:	n/a
50	chr3:347869-347919	HPAEpiC	pulmonary alveolar:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:297411..299702-chr3:300779..302869,2	K562	blood:
2	chr3:321596..323780-chr3:337949..340526,2	MCF-7	breast:
3	chr3:333238..334968-chr3:337821..339342,2	MCF-7	breast:
4	chr3:321596..323780-chr3:337949..340526,2	MCF-7	breast:
5	chr3:333238..334968-chr3:337821..339342,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-1194P	TF binding region
RNU6-1194P	CpG island

Extended variants
information (count: 2279 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:2279 , 50 per page) page: 1 2 3 4 5 6 7 ... 46

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs563130425	chr3:301083-301084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs191762030	chr3:301090-301091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs574781002	chr3:301106-301107	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs150856473	chr3:301107-301108	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs79601149	chr3:301130-301131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs574399977	chr3:301147-301148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs188921024	chr3:301167-301168	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs556523624	chr3:301168-301169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs192592613	chr3:301185-301186	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs577990171	chr3:301212-301213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs183470154	chr3:301289-301290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs73815804	chr3:301293-301294	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs377363809	chr3:301296-301297	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs139833071	chr3:301298-301299	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs556746416	chr3:301312-301313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs186690968	chr3:301326-301327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs560822996	chr3:301347-301348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs564192414	chr3:301351-301352	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs11920276	chr3:301361-301362	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs372777798	chr3:301372-301373	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs191463939	chr3:301373-301374	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs77286176	chr3:301377-301378	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs13066151	chr3:301385-301386	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs12633018	chr3:301422-301423	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs200457519	chr3:301486-301487	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs376142245	chr3:301490-301491	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs570358672	chr3:301491-301492	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs183897021	chr3:301508-301509	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs537766394	chr3:301540-301541	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs564397652	chr3:301543-301544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs73092555	chr3:301569-301570	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs17015118	chr3:301592-301593	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs145379928	chr3:301616-301617	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs374094750	chr3:301619-301620	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs17015134	chr3:301656-301657	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs541489591	chr3:301669-301670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs569076428	chr3:301703-301704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs577948645	chr3:301706-301707	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs73092559	chr3:301721-301722	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs57125941	chr3:301750-301751	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs139817018	chr3:301817-301818	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs189726289	chr3:301845-301846	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs554355639	chr3:301865-301866	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs372381629	chr3:301888-301889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs113349535	chr3:301912-301913	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs71619443	chr3:301916-301917	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs57197219	chr3:301919-301920	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs542840405	chr3:301924-301925	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs370689021	chr3:301946-301947	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs58225264	chr3:301966-301967	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD

Chromatin state (count:181 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:285400-307400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:286200-315400	Weak transcription	Ovary	ovary
3	chr3:291800-305200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:297600-302600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:300000-305200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:300200-304600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:301000-302000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:301000-302200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:301000-304800	Weak transcription	Fetal Brain Male	brain
10	chr3:302000-303400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:302200-303200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:302400-306200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:302600-303200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:303200-305600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:303200-306000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:303400-304400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:304400-307600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:304600-304800	Enhancers	Fetal Brain Female	brain
19	chr3:304600-307000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:304800-305800	Enhancers	Fetal Brain Male	brain
21	chr3:305000-307800	Enhancers	HepG2	liver
22	chr3:305200-305800	Enhancers	Brain Germinal Matrix	brain
23	chr3:305400-307800	Enhancers	Hela-S3	cervix
24	chr3:305600-305800	Enhancers	HMEC	breast
25	chr3:305600-306000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:305600-307000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:305800-306200	Enhancers	A549	lung
28	chr3:305800-306400	Weak transcription	HMEC	breast
29	chr3:305800-306800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:305800-308400	Weak transcription	Fetal Brain Male	brain
31	chr3:305800-308600	Weak transcription	Brain Germinal Matrix	brain
32	chr3:306000-307400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:306200-306400	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr3:306200-306800	Flanking Active TSS	A549	lung
35	chr3:306400-306600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:306400-306800	Enhancers	Brain Substantia Nigra	brain
37	chr3:306400-307000	Enhancers	HMEC	breast
38	chr3:306600-306800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:306600-307000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:306600-307000	Enhancers	NH-A	brain
41	chr3:306800-308400	Enhancers	A549	lung
42	chr3:307000-318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:308400-308800	Enhancers	Fetal Brain Male	brain
44	chr3:308600-309000	Enhancers	Brain Germinal Matrix	brain
45	chr3:308800-318200	Weak transcription	Fetal Brain Male	brain
46	chr3:309000-312400	Weak transcription	Brain Germinal Matrix	brain
47	chr3:312000-313400	Enhancers	Primary B cells from peripheral blood	blood
48	chr3:312000-313600	Enhancers	Primary B cells from cord blood	blood
49	chr3:313400-314400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:313600-314000	Weak transcription	Primary B cells from cord blood	blood

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