Variant report

Variant	esv3490810
Chromosome Location	chr4:74312285-74312478
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	chr4:74312019-74312467	HepG2	liver:	n/a	n/a
2	ARID3A	chr4:74312080-74312468	K562	blood:	n/a	n/a
3	BHLHE40	chr4:74312107-74312322	GM12878	blood:	n/a	n/a
4	CTCF	chr4:74312400-74312550	HRE	kidney:	n/a	n/a
5	CTCF	chr4:74312160-74312310	GM06990	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
6	CTCF	chr4:74312140-74312290	GM12872	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
7	CTCF	chr4:74312011-74312577	ECC-1	luminal epithelium:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
8	CTCF	chr4:74312380-74312530	GM12873	blood:	n/a	n/a
9	CTCF	chr4:74312360-74312510	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr4:74312200-74312350	GM12869	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
11	CTCF	chr4:74312420-74312570	AG09319	gingival:	n/a	n/a
12	CTCF	chr4:74312440-74312590	HMEC	breast:	n/a	n/a
13	CTCF	chr4:74312200-74312350	GM12870	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
14	CTCF	chr4:74312160-74312310	AG10803	skin:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
15	CTCF	chr4:74312140-74312290	HVMF	connective:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
16	CTCF	chr4:74312180-74312330	HVMF	connective:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
17	CTCF	chr4:74311941-74312599	MCF-7	breast:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
18	CTCF	chr4:74311938-74312572	A549	lung:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
19	CTCF	chr4:74312065-74312340	HepG2	liver:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
20	CTCF	chr4:74312160-74312310	AoAF	blood vessel:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
21	CTCF	chr4:74312420-74312570	HA-sp	spinal cord:	n/a	n/a
22	CTCF	chr4:74312118-74312444	MCF-7	breast:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
23	CTCF	chr4:74312400-74312550	AG09319	gingival:	n/a	n/a
24	CTCF	chr4:74311897-74312595	K562	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
25	CTCF	chr4:74312160-74312310	GM12873	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
26	CTCF	chr4:74312420-74312570	HEEpiC	esophagus:	n/a	n/a
27	CTCF	chr4:74312440-74312590	SAEC	small airway:	n/a	n/a
28	CTCF	chr4:74312440-74312590	AG10803	skin:	n/a	n/a
29	CTCF	chr4:74312420-74312570	HCT-116	colon:	n/a	n/a
30	CTCF	chr4:74312128-74312435	Lung_OC	lung:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
31	CTCF	chr4:74312180-74312330	GM12867	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
32	CTCF	chr4:74312160-74312310	HL-60	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
33	CTCF	chr4:74312160-74312310	HFF-Myc	foreskin:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
34	CTCF	chr4:74312021-74312418	A549	lung:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
35	CTCF	chr4:74312140-74312290	WERI-Rb-1	eye:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
36	CTCF	chr4:74312160-74312310	HCM	heart:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
37	CTCF	chr4:74311822-74312712	A549	lung:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
38	CTCF	chr4:74312123-74312432	Kidney_OC	kidney:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
39	CTCF	chr4:74312109-74312459	Medullo	brain:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
40	CTCF	chr4:74312140-74312290	K562	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
41	CTCF	chr4:74312124-74312437	GM10248	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
42	CTCF	chr4:74312090-74312465	GM12878	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
43	CTCF	chr4:74312380-74312530	GM12801	blood:	n/a	n/a
44	CTCF	chr4:74312111-74312437	Hela-S3	cervix:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
45	CTCF	chr4:74311703-74312560	K562	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
46	CTCF	chr4:74312180-74312330	BE2_C	brain:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
47	CTCF	chr4:74312420-74312570	AG09309	skin:	n/a	n/a
48	CTCF	chr4:74312400-74312550	HPAF	blood vessel:	n/a	n/a
49	CTCF	chr4:74312160-74312310	Hela-S3	cervix:	n/a	chr4:74312258-74312279 chr4:74312263-74312281
50	CTCF	chr4:74312105-74312439	K562	blood:	n/a	chr4:74312258-74312279 chr4:74312263-74312281

No.	Distal block	Cell Line	Cell type
1	chr4:74177054..74177984-chr4:74311787..74312670,5	MCF-7	breast:
2	chr4:74311780..74312697-chr4:74519035..74519771,3	MCF-7	breast:
3	chr4:74176660..74177830-chr4:74312110..74312752,4	MCF-7	breast:
4	chr4:74206756..74207673-chr4:74311795..74312505,4	K562	blood:
5	chr4:74207042..74207824-chr4:74311798..74312657,3	MCF-7	breast:
6	chr4:74300190..74300741-chr4:74311556..74312309,2	MCF-7	breast:
7	chr4:74206401..74207863-chr4:74311210..74313292,12	MCF-7	breast:

Variant related genes	Relation type
AFP	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536392979	chr4:74312312-74312313	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs11941100	chr4:74312340-74312341	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs573365309	chr4:74312343-74312344	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs372296626	chr4:74312360-74312361	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs376832215	chr4:74312361-74312362	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs369479119	chr4:74312362-74312363	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs28693791	chr4:74312368-74312369	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs201109826	chr4:74312373-74312374	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs59865758	chr4:74312374-74312375	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs182936735	chr4:74312404-74312405	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs559011893	chr4:74312407-74312408	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:80)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Colorectal cancer	16272173	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	16573809	CNVD
Osteoporosis	18992858	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Multiple myeloma	17550852	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Myelofibrosis	22110671	CNVD
Abnormal phenotypes	18644119	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Intracranial aneurysm	16715129	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ovarian cancer	21720365	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74303400-74317200	Weak transcription	Fetal Intestine Large	intestine
2	chr4:74303600-74315800	Weak transcription	Fetal Intestine Small	intestine
3	chr4:74308400-74313400	Weak transcription	NH-A	brain
4	chr4:74308600-74313000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:74309600-74315400	Genic enhancers	HepG2	liver
6	chr4:74310000-74315200	Enhancers	Liver	Liver
7	chr4:74311000-74316000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:74311200-74313400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:74311400-74316400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr4:74311600-74314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:74312200-74313200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:74312200-74313200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:74312200-74313200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:74312200-74314800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:74312400-74312800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:74312400-74314000	Enhancers	NHEK	skin

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