Variant report

Variant	esv3435550
Chromosome Location	chr2:53069350-53092313
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	CEBPB	chr2:53089862-53090309	A549	lung:	n/a	chr2:53090036-53090044
2	E2F4	chr2:53077514-53077601	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr2:53089825-53090361	A549	lung:	n/a	n/a
4	EP300	chr2:53070214-53070237	GM12878	blood:	n/a	n/a
5	EP300	chr2:53089930-53090244	Hela-S3	cervix:	n/a	n/a
6	FOS	chr2:53089953-53090275	MCF10A-Er-Src	breast:	n/a	chr2:53090034-53090043
7	FOS	chr2:53092183-53092504	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr2:53089817-53090312	MCF10A-Er-Src	breast:	n/a	chr2:53090034-53090043
9	FOS	chr2:53089862-53090311	MCF10A-Er-Src	breast:	n/a	chr2:53090034-53090043
10	FOS	chr2:53092191-53092498	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr2:53089963-53090297	MCF10A-Er-Src	breast:	n/a	chr2:53090034-53090043
12	FOS	chr2:53084924-53085177	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr2:53084937-53085214	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr2:53092299-53092392	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr2:53092199-53092458	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr2:53085031-53085087	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr2:53085048-53085139	MCF10A-Er-Src	breast:	n/a	n/a
18	FOSL1	chr2:53089892-53090397	HCT-116	colon:	n/a	chr2:53090034-53090043
19	FOSL1	chr2:53089914-53090419	HCT-116	colon:	n/a	chr2:53090034-53090043
20	FOSL2	chr2:53089855-53090313	A549	lung:	n/a	chr2:53090034-53090043
21	FOSL2	chr2:53089967-53090291	A549	lung:	n/a	chr2:53090034-53090043
22	GATA3	chr2:53080577-53080773	SH-SY5Y	brain:	n/a	n/a
23	GATA3	chr2:53089763-53090368	A549	lung:	n/a	chr2:53090311-53090318
24	JUN	chr2:53072224-53072454	HepG2	liver:	n/a	chr2:53072340-53072353
25	JUND	chr2:53072172-53072525	HepG2	liver:	n/a	n/a
26	JUND	chr2:53089837-53090386	HCT-116	colon:	n/a	chr2:53090034-53090043
27	JUND	chr2:53089962-53090384	HCT-116	colon:	n/a	chr2:53090034-53090043
28	MAFK	chr2:53078389-53078494	HepG2	liver:	n/a	n/a
29	MAX	chr2:53071942-53072142	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAZ	chr2:53088929-53088932	HepG2	liver:	n/a	n/a
31	MYC	chr2:53085463-53085481	NB4	blood:	n/a	n/a
32	MYC	chr2:53087143-53087154	NB4	blood:	n/a	n/a
33	POLR2A	chr2:53079743-53080155	A549	lung:	n/a	n/a
34	POLR2A	chr2:53088954-53089121	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr2:53079534-53079541	A549	lung:	n/a	n/a
36	POLR2A	chr2:53079827-53079855	MCF-7	breast:	n/a	n/a
37	POLR2A	chr2:53073157-53073332	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr2:53079800-53079889	MCF-7	breast:	n/a	n/a
39	POLR2A	chr2:53079812-53079819	MCF-7	breast:	n/a	n/a
40	POLR2A	chr2:53079858-53080083	MCF-7	breast:	n/a	n/a
41	POLR2A	chr2:53071859-53072056	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr2:53079794-53079798	MCF-7	breast:	n/a	n/a
43	POLR2A	chr2:53079455-53079481	A549	lung:	n/a	n/a
44	POLR2A	chr2:53079505-53079530	A549	lung:	n/a	n/a
45	POLR2A	chr2:53079929-53080077	MCF-7	breast:	n/a	n/a
46	SP1	chr2:53089857-53090428	A549	lung:	n/a	n/a
47	SP1	chr2:53089921-53090352	A549	lung:	n/a	n/a
48	SP1	chr2:53089815-53090476	HCT-116	colon:	n/a	n/a
49	STAT3	chr2:53089827-53090325	MCF10A-Er-Src	breast:	n/a	chr2:53090130-53090139 chr2:53090131-53090140
50	STAT3	chr2:53092189-53092498	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC2-1	chr2:53091373-53091454	XLOC_001470

Variant related genes	Relation type
ENSG00000232604	TF binding region

Extended variants
information (count: 479 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:479 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs75397928	chr2:53071403-53071404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs12614827	chr2:53071428-53071429	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs535445656	chr2:53071445-53071446	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs142226492	chr2:53071451-53071452	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs559067501	chr2:53071461-53071462	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs549009750	chr2:53071485-53071486	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs563037322	chr2:53071491-53071492	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs70944106	chr2:53071550-53071551	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs12611901	chr2:53071693-53071694	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs200279101	chr2:53071714-53071715	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs541656633	chr2:53071757-53071758	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs12621401	chr2:53071780-53071781	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs528986288	chr2:53071781-53071782	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs180983198	chr2:53071785-53071786	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs187328915	chr2:53071792-53071793	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs531588843	chr2:53071839-53071840	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs534165491	chr2:53071925-53071926	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs553097565	chr2:53071946-53071947	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs78436075	chr2:53071992-53071993	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs192101176	chr2:53072041-53072042	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs573022855	chr2:53072048-53072049	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs547640825	chr2:53072075-53072076	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs536760797	chr2:53072106-53072107	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs556571284	chr2:53072110-53072111	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs116810536	chr2:53072115-53072116	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs12713224	chr2:53072134-53072135	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs558983283	chr2:53072155-53072156	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs572727066	chr2:53072203-53072204	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs555363253	chr2:53072229-53072230	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs183471923	chr2:53072315-53072316	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs554756198	chr2:53072337-53072338	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs570152622	chr2:53072350-53072351	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs375769310	chr2:53079418-53079419	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs534582973	chr2:53079438-53079439	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs547892190	chr2:53079440-53079441	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs34143436	chr2:53079450-53079451	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs568317135	chr2:53079451-53079452	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs551543457	chr2:53079452-53079453	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs536949311	chr2:53079453-53079454	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs530954927	chr2:53079458-53079459	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs557078118	chr2:53079459-53079460	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs570305422	chr2:53079460-53079461	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs539295088	chr2:53079476-53079477	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs553029192	chr2:53079482-53079483	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs191392293	chr2:53079508-53079509	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs573035927	chr2:53079548-53079549	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs542174598	chr2:53079564-53079565	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs546943890	chr2:53079574-53079575	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs555500981	chr2:53079585-53079586	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs575851255	chr2:53079595-53079596	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53071400-53072000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr2:53071400-53072000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr2:53071800-53072400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr2:53072000-53072400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr2:53079400-53080400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:53083200-53083400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:53083800-53085800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:53085800-53090600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:53087400-53088000	Enhancers	A549	lung
10	chr2:53088000-53088800	Weak transcription	A549	lung
11	chr2:53088600-53090400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:53088800-53089000	Enhancers	A549	lung
13	chr2:53089000-53089400	Weak transcription	A549	lung
14	chr2:53089400-53090200	Enhancers	A549	lung
15	chr2:53089800-53090200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:53089800-53090200	Weak transcription	NHDF-Ad	bronchial
17	chr2:53090200-53090400	Enhancers	NHDF-Ad	bronchial
18	chr2:53090200-53091000	Weak transcription	A549	lung
19	chr2:53090200-53093600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:53090400-53091800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:53090400-53096200	Weak transcription	NHDF-Ad	bronchial
22	chr2:53090600-53091000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:53091000-53091200	Enhancers	A549	lung
24	chr2:53091600-53095600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:53091800-53092600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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