Variant report

Variant	esv3381714
Chromosome Location	chr1:152634322-152646230
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	BHLHE40	chr1:152635566-152635930	HepG2	liver:	n/a	chr1:152635767-152635776 chr1:152635766-152635775 chr1:152635766-152635775
2	CEBPB	chr1:152635735-152635823	HepG2	liver:	n/a	chr1:152635776-152635787 chr1:152635777-152635788
3	CEBPB	chr1:152645918-152646083	A549	lung:	n/a	chr1:152645928-152645939 chr1:152645930-152645941 chr1:152645928-152645941 chr1:152646021-152646034 chr1:152645928-152645941
4	CEBPB	chr1:152645885-152646048	HepG2	liver:	n/a	chr1:152645928-152645939 chr1:152645930-152645941 chr1:152645928-152645941 chr1:152646021-152646034 chr1:152645928-152645941
5	CEBPB	chr1:152645922-152646032	K562	blood:	n/a	chr1:152645928-152645939 chr1:152645930-152645941 chr1:152645928-152645941 chr1:152645928-152645941
6	CTCF	chr1:152638933-152639008	GM20000	blood:	n/a	n/a
7	CTCF	chr1:152638220-152638370	GM12867	blood:	n/a	n/a
8	FOS	chr1:152644644-152644748	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:152645515-152645721	MCF10A-Er-Src	breast:	n/a	chr1:152645656-152645664 chr1:152645655-152645665
10	FOS	chr1:152645503-152645789	MCF10A-Er-Src	breast:	n/a	chr1:152645656-152645664 chr1:152645655-152645665
11	MAFK	chr1:152634487-152634566	HepG2	liver:	n/a	chr1:152634492-152634512 chr1:152634496-152634506
12	POLR2A	chr1:152644383-152644437	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:152645648-152645658	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:152643039-152643139	A549	lung:	n/a	n/a
15	POLR2A	chr1:152645659-152645871	GM12878	blood:	n/a	n/a
16	STAT3	chr1:152645631-152645633	MCF10A-Er-Src	breast:	n/a	n/a
17	STAT3	chr1:152634854-152634857	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr1:152645608-152645679	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:152636074-152636124	HAEpiC	amniotic membrane:	n/a
2	chr1:152636074-152636124	CMK	blood:	n/a
3	chr1:152635878-152635928	ECC-1	luminal epithelium:	n/a
4	chr1:152635200-152635250	AoSMC	blood vessel:	n/a
5	chr1:152635200-152635250	H1-hESC	embryonic stem cell:	embryo
6	chr1:152635226-152635276	SK-N-SH_RA	brain:	n/a
7	chr1:152636834-152636884	PFSK-1	brain:	n/a
8	chr1:152635226-152635276	ECC-1	luminal epithelium:	n/a
9	chr1:152635878-152635928	H1-hESC	embryonic stem cell:	embryo
10	chr1:152635878-152635928	T-47D	breast:	n/a
11	chr1:152635200-152635250	Jurkat	blood:	n/a
12	chr1:152635878-152635928	HCF	heart:	n/a
13	chr1:152635226-152635276	MCF10A-Er-Src	breast:	n/a
14	chr1:152636074-152636124	Caco-2	colon:	n/a
15	chr1:152635878-152635928	RPTEC	kidney:	n/a
16	chr1:152636834-152636884	SKMC	muscle:	n/a
17	chr1:152636834-152636884	BE2_C	brain:	n/a
18	chr1:152635226-152635276	HPAEpiC	pulmonary alveolar:	n/a
19	chr1:152635200-152635250	PrEC	prostate:	n/a
20	chr1:152636074-152636124	A549	lung:	n/a
21	chr1:152635226-152635276	BE2_C	brain:	n/a
22	chr1:152635226-152635276	SKMC	muscle:	n/a
23	chr1:152636074-152636124	GM12891	blood:	n/a
24	chr1:152636834-152636884	AG04450	lung:	fetal
25	chr1:152635200-152635250	MCF10A-Er-Src	breast:	n/a
26	chr1:152635226-152635276	HepG2	liver:	n/a
27	chr1:152636074-152636124	AG10803	skin:	n/a
28	chr1:152636834-152636884	LNCaP	prostate:	n/a
29	chr1:152636074-152636124	AG04449	skin:	fetal
30	chr1:152636834-152636884	ECC-1	luminal epithelium:	n/a
31	chr1:152635226-152635276	HUVEC	blood vessel:	n/a
32	chr1:152636834-152636884	HRCEpiC	kidney:	n/a
33	chr1:152636834-152636884	SK-N-SH	brain:	n/a
34	chr1:152636074-152636124	HCPEpiC	choroid plexus:	n/a
35	chr1:152635878-152635928	HCPEpiC	choroid plexus:	n/a
36	chr1:152635226-152635276	NHDF-neo	bronchial:	n/a
37	chr1:152636074-152636124	HPAEpiC	pulmonary alveolar:	n/a
38	chr1:152636074-152636124	HEEpiC	esophagus:	n/a
39	chr1:152636834-152636884	HCPEpiC	choroid plexus:	n/a
40	chr1:152635226-152635276	U87	brain:	n/a
41	chr1:152636834-152636884	A549	lung:	n/a
42	chr1:152635878-152635928	ProgFib	skin:	n/a
43	chr1:152635226-152635276	Jurkat	blood:	n/a
44	chr1:152635226-152635276	AG10803	skin:	n/a
45	chr1:152635200-152635250	AG04449	skin:	fetal
46	chr1:152635200-152635250	NH-A	brain:	n/a
47	chr1:152636074-152636124	LNCaP	prostate:	n/a
48	chr1:152635200-152635250	HCT-116	colon:	n/a
49	chr1:152635200-152635250	NT2-D1	testis:	n/a
50	chr1:152636074-152636124	GM12892	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:152632060..152634840-chr1:152638354..152640760,3	MCF-7	breast:
2	chr1:152632060..152634840-chr1:152638354..152640760,3	MCF-7	breast:
3	chr1:152636333..152638200-chr1:152640382..152642343,2	K562	blood:
4	chr1:152636333..152638200-chr1:152640382..152642343,2	K562	blood:
5	chr1:152640283..152643005-chr1:152645549..152648170,2	MCF-7	breast:

Variant related genes	Relation type
LCE2C	TF binding region
LCE2D	TF binding region
LCE2B	TF binding region
LCE2C	CpG island
LCE2D	CpG island
LCE2B	CpG island
ENSG00000187180	chromatin interactions

Extended variants
information (count: 148 )
Associated
traits (count: 121 )

Variant overlapped rSNPs/rCNVs (count:148 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs567885598	chr1:152634487-152634488	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs556849268	chr1:152634490-152634491	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs11205062	chr1:152635201-152635202	Inactive region	CpG island	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs550114640	chr1:152635226-152635227	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
5	rs76758919	chr1:152635566-152635567	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs576608608	chr1:152635580-152635581	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs545729508	chr1:152635728-152635729	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs531010752	chr1:152635764-152635765	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs528132417	chr1:152635810-152635811	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs576466937	chr1:152635825-152635826	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs535003368	chr1:152635827-152635828	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs377065170	chr1:152635828-152635829	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs376744824	chr1:152635838-152635839	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs561683366	chr1:152635870-152635871	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs1831637	chr1:152640287-152640288	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs189590798	chr1:152640457-152640458	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs567816239	chr1:152640508-152640509	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs536971004	chr1:152640548-152640549	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs73009164	chr1:152640584-152640585	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs370580449	chr1:152640593-152640594	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs181528503	chr1:152640598-152640599	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs570108219	chr1:152640602-152640603	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs372877604	chr1:152640732-152640733	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs542358244	chr1:152640748-152640749	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs539033457	chr1:152640754-152640755	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs528731817	chr1:152640769-152640770	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs558866004	chr1:152640785-152640786	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs77313071	chr1:152640789-152640790	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs76085548	chr1:152640864-152640865	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs554489989	chr1:152640869-152640870	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs141628392	chr1:152640889-152640890	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs76428162	chr1:152640893-152640894	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs72702855	chr1:152640981-152640982	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs185984004	chr1:152641004-152641005	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs545489727	chr1:152641047-152641048	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs143471753	chr1:152641083-152641084	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs552537872	chr1:152641116-152641117	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs528193884	chr1:152641120-152641121	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs189130305	chr1:152641134-152641135	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs567800218	chr1:152641179-152641180	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs564035272	chr1:152641200-152641201	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs550543842	chr1:152641209-152641210	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs7541676	chr1:152641341-152641342	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs72506300	chr1:152641342-152641343	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs377220698	chr1:152641348-152641349	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs398074312	chr1:152641349-152641350	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs539300527	chr1:152641399-152641400	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs552306020	chr1:152641443-152641444	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs531615407	chr1:152641491-152641492	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs566037781	chr1:152641497-152641498	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:121)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	21129771	CNVD
Non-small cell lung cancer	21385341	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Ewing''s sarcoma	21437220	CNVD
Liposarcoma	21253554	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Breast cancer	20409316	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Glioblastoma multiforme	21080181	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Lung cancer	18438408	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Systemic lupus erythematosus	21956041	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Non-small cell lung cancer	21829676	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	17899364	CNVD
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21611746	CNVD
Retinoblastoma	19183342	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Ewing''s sarcoma	17952124	CNVD
Osteosarcoma	17242211	CNVD
Ovarian cancer	17242211	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Schizophrenia	18990708	CNVD
Sudden cardiac death	19188705	CNVD
Plasma-cell dyscrasia	16705089	CNVD
Myeloma	17024118	CNVD
Cancer	17060936	CNVD
Multiple myeloma	16616336	CNVD
Type 2 diabetes	19141583	CNVD
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Burkitt''s lymphoma	19759907	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	18703704	CNVD
Breast cancer	21509527	CNVD
Bladder cancer	21909424	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Myelofibrosis	22110671	CNVD
Liver carcinoma	19366792	CNVD
Testicular germ cell tumor	18059402	CNVD
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Gastrointestinal cancer	16790693	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Glioblastoma multiforme	21138945	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Pancreatic cancer	17952125	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	22522925	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152635600-152635800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:152643000-152643200	Enhancers	Esophagus	oesophagus
3	chr1:152645800-152646000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:152646200-152649000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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