Variant report

Variant	esv3425363
Chromosome Location	chr3:50056273-50063031
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50057660..50059872-chr6:31709500..31711893,2	K562	blood:
2	chr3:50037509..50039299-chr3:50062748..50064702,2	MCF-7	breast:
3	chr3:50060113..50061890-chr3:50064863..50067741,2	K562	blood:

Variant related genes	Relation type
ENSG00000204410	chromatin interactions

Extended variants
information (count: 251 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:251 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557932943	chr3:50056343-50056344	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs544269245	chr3:50056375-50056376	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs185457517	chr3:50056404-50056405	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs545020376	chr3:50056421-50056422	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs139198283	chr3:50056435-50056436	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs55702230	chr3:50056459-50056460	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs575425991	chr3:50056476-50056477	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs75729494	chr3:50056478-50056479	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs189819148	chr3:50056479-50056480	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs555997522	chr3:50056482-50056483	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs180779707	chr3:50056526-50056527	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs185938472	chr3:50056589-50056590	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs564280985	chr3:50056662-50056663	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs142756007	chr3:50056705-50056706	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs540695065	chr3:50056733-50056734	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs146947777	chr3:50056734-50056735	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs192029223	chr3:50056834-50056835	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs550996117	chr3:50056969-50056970	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs569569444	chr3:50056973-50056974	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs147986395	chr3:50056984-50056985	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs7629384	chr3:50057037-50057038	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs566597316	chr3:50057058-50057059	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs533669470	chr3:50057113-50057114	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs150597809	chr3:50057124-50057125	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs567158200	chr3:50057127-50057128	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs183859594	chr3:50057182-50057183	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs139616696	chr3:50057184-50057185	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs564852429	chr3:50057198-50057199	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs556083158	chr3:50057212-50057213	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs34185097	chr3:50057232-50057233	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs527299355	chr3:50057234-50057235	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs576124353	chr3:50057242-50057243	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs553572983	chr3:50057248-50057249	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs564935798	chr3:50057327-50057328	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs373832168	chr3:50057342-50057343	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs34579493	chr3:50057372-50057373	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs572172123	chr3:50057388-50057389	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs540382722	chr3:50057410-50057411	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs562166042	chr3:50057467-50057468	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs6799579	chr3:50057500-50057501	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs56731561	chr3:50057515-50057516	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs555125348	chr3:50057516-50057517	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs188404263	chr3:50057563-50057564	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs190610848	chr3:50057619-50057620	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs533648028	chr3:50057626-50057627	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs550306018	chr3:50057673-50057674	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs568865210	chr3:50057676-50057677	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs529670728	chr3:50057724-50057725	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs146243973	chr3:50057733-50057734	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs567083204	chr3:50057763-50057764	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:100)

Disease	PMID	Source
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
Glioblastoma multiforme	21080181	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
Oral squamous cell carcinoma	17134496	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Adrenocortical carcinoma	18281524	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
early-passage human iPS cells	21368824	CNVD
Cancer	20164919	CNVD

Chromatin state (count:287 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:49998400-50078600	Weak transcription	K562	blood
3	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50006000-50064000	Weak transcription	Stomach Mucosa	stomach
5	chr3:50010800-50087000	Weak transcription	NHLF	lung
6	chr3:50011000-50078400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:50011000-50091600	Weak transcription	Colonic Mucosa	Colon
8	chr3:50015200-50092000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:50028000-50056400	Weak transcription	Ovary	ovary
10	chr3:50028800-50082600	Weak transcription	Right Ventricle	heart
11	chr3:50030200-50065600	Weak transcription	Fetal Heart	heart
12	chr3:50035200-50058200	Weak transcription	Esophagus	oesophagus
13	chr3:50036600-50085600	Weak transcription	HUVEC	blood vessel
14	chr3:50037200-50087000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:50037600-50061800	Weak transcription	Small Intestine	intestine
16	chr3:50038400-50084600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:50038600-50087400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:50038800-50056800	Weak transcription	HepG2	liver
19	chr3:50039400-50061800	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:50039400-50084600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:50041400-50057000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:50041400-50095200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:50041600-50056800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:50041600-50057000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:50041600-50058200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:50041600-50061600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:50041600-50063000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:50041600-50065200	Weak transcription	NH-A	brain
29	chr3:50041600-50085000	Weak transcription	Fetal Brain Female	brain
30	chr3:50041600-50085400	Weak transcription	Brain Angular Gyrus	brain
31	chr3:50041600-50093400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:50041800-50085200	Weak transcription	Fetal Brain Male	brain
33	chr3:50043400-50085200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:50044000-50057400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:50045200-50085000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:50046200-50059000	Strong transcription	Dnd41	blood
37	chr3:50046800-50056600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:50046800-50056600	Weak transcription	Osteobl	bone
39	chr3:50046800-50064600	Weak transcription	Aorta	Aorta
40	chr3:50046800-50065400	Weak transcription	Fetal Kidney	kidney
41	chr3:50046800-50085800	Weak transcription	HMEC	breast
42	chr3:50047000-50061400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:50047200-50057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:50047200-50085200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:50047200-50085400	Weak transcription	Left Ventricle	heart
46	chr3:50047200-50092600	Weak transcription	Gastric	stomach
47	chr3:50047400-50085000	Weak transcription	Lung	lung
48	chr3:50048800-50057800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:50048800-50060200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:50048800-50085600	Weak transcription	A549	lung

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