Variant report

Variant	esv3367160
Chromosome Location	chr4:30719345-30719641
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	BACH1	chr4:30719116-30720035	H1-hESC	embryonic stem cell:	n/a	n/a
2	BRCA1	chr4:30719262-30719497	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr4:30718313-30719670	Hela-S3	cervix:	n/a	chr4:30719469-30719480 chr4:30719469-30719480 chr4:30719467-30719480
4	CEBPB	chr4:30719236-30719501	H1-hESC	embryonic stem cell:	n/a	chr4:30719469-30719480 chr4:30719469-30719480 chr4:30719467-30719480
5	CHD1	chr4:30719042-30720057	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr4:30718962-30719608	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD2	chr4:30718465-30719796	Hela-S3	cervix:	n/a	chr4:30718947-30718957
8	CTBP2	chr4:30718734-30724882	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr4:30719240-30719390	AG04450	lung:	n/a	n/a
10	CTCF	chr4:30719440-30719590	HPAF	blood vessel:	n/a	n/a
11	CTCF	chr4:30719540-30719690	AoAF	blood vessel:	n/a	n/a
12	CTCF	chr4:30719320-30719470	NHEK	skin:	n/a	n/a
13	CTCF	chr4:30719480-30719630	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr4:30719360-30719510	HRPEpiC	eye:	n/a	n/a
15	CTCF	chr4:30719222-30719693	IMR90	lung:	n/a	n/a
16	CTCF	chr4:30719440-30719590	SAEC	small airway:	n/a	n/a
17	CTCF	chr4:30719460-30719610	AG04450	lung:	n/a	n/a
18	CTCF	chr4:30719440-30719590	HEEpiC	esophagus:	n/a	n/a
19	CTCF	chr4:30719469-30719593	MCF-7	breast:	n/a	n/a
20	CTCF	chr4:30719460-30719610	AoAF	blood vessel:	n/a	n/a
21	CTCF	chr4:30719440-30719590	HBMEC	blood vessel:	n/a	n/a
22	CTCF	chr4:30719360-30719510	HPAF	blood vessel:	n/a	n/a
23	CTCF	chr4:30719320-30719470	HCPEpiC	choroid plexus:	n/a	n/a
24	CTCF	chr4:30719380-30719530	HAc	cerebellar:	n/a	n/a
25	CTCF	chr4:30719502-30719563	NHEK	skin:	n/a	n/a
26	CTCF	chr4:30719400-30719550	GM12874	blood:	n/a	n/a
27	CTCF	chr4:30719480-30719630	BJ	skin:	n/a	n/a
28	CTCF	chr4:30719580-30719730	HPAF	blood vessel:	n/a	n/a
29	CTCF	chr4:30719480-30719630	GM12871	blood:	n/a	n/a
30	CTCF	chr4:30719200-30719350	AG04450	lung:	n/a	n/a
31	E2F1	chr4:30718790-30719537	Hela-S3	cervix:	n/a	chr4:30718913-30718923 chr4:30719320-30719331
32	E2F4	chr4:30718863-30720161	MCF10A-Er-Src	breast:	n/a	chr4:30718913-30718923 chr4:30719721-30719730
33	E2F6	chr4:30718907-30720192	H1-hESC	embryonic stem cell:	n/a	chr4:30718913-30718923 chr4:30719721-30719730
34	E2F6	chr4:30718890-30720359	H1-hESC	embryonic stem cell:	n/a	chr4:30718913-30718923 chr4:30719721-30719730
35	EGR1	chr4:30719083-30719894	H1-hESC	embryonic stem cell:	n/a	chr4:30719722-30719735 chr4:30719311-30719322 chr4:30719309-30719324 chr4:30719717-30719726 chr4:30719196-30719206 chr4:30719716-30719729 chr4:30719305-30719327 chr4:30719310-30719323 chr4:30719720-30719730
36	FOS	chr4:30719082-30720238	HUVEC	blood vessel:	n/a	n/a
37	GATA2	chr4:30719520-30720198	SH-SY5Y	brain:	n/a	n/a
38	GATA2	chr4:30719640-30720192	HUVEC	blood vessel:	n/a	n/a
39	GTF2F1	chr4:30718545-30719598	Hela-S3	cervix:	n/a	n/a
40	HA-E2F1	chr4:30718862-30720240	MCF-7	breast:	n/a	chr4:30718913-30718923 chr4:30719320-30719331 chr4:30719721-30719730
41	HA-E2F1	chr4:30718763-30720005	Hela-S3	cervix:	n/a	chr4:30718913-30718923 chr4:30719320-30719331 chr4:30719721-30719730
42	JUND	chr4:30719449-30719451	H1-hESC	embryonic stem cell:	n/a	n/a
43	KAP1	chr4:30719081-30722695	HEK293	kidney:	n/a	chr4:30722261-30722269 chr4:30722198-30722206
44	KAP1	chr4:30719234-30720127	U2OS	brain:	n/a	n/a
45	MAFK	chr4:30719618-30720017	Hela-S3	cervix:	n/a	n/a
46	MAFK	chr4:30718761-30720187	IMR90	lung:	n/a	chr4:30718764-30718775 chr4:30718765-30718776 chr4:30718764-30718775
47	MAFK	chr4:30718843-30719360	Hela-S3	cervix:	n/a	n/a
48	MAX	chr4:30718413-30720197	Hela-S3	cervix:	n/a	n/a
49	MAX	chr4:30718913-30720025	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr4:30718805-30720206	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PCDH7	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs188953242	chr4:30719345-30719346	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs116589863	chr4:30719372-30719373	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs527509361	chr4:30719373-30719374	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs548523659	chr4:30719384-30719385	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs566933270	chr4:30719403-30719404	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs537513084	chr4:30719415-30719416	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs549485610	chr4:30719419-30719420	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs571330347	chr4:30719442-30719443	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs538859743	chr4:30719456-30719457	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs369643151	chr4:30719465-30719466	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs373084044	chr4:30719471-30719472	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs73117586	chr4:30719490-30719491	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs79994847	chr4:30719492-30719493	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs546763325	chr4:30719509-30719510	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs375048982	chr4:30719531-30719532	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs554971036	chr4:30719532-30719533	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs3756024	chr4:30719559-30719560	Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs543914022	chr4:30719610-30719611	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
Oral squamous cell carcinoma	17134496	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Lung cancer	18438408	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Cancer	21183584	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
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Olfactory neuroblastoma	18408657	CNVD
Cancer	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Prostate cancer	16573809	CNVD
Myelofibrosis	22110671	CNVD
Tetralogy of Fallot	22912587	CNVD
Renal cell carcinoma	18194544	CNVD
Colorectal cancer	16774939	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:166 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:30717600-30724000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:30717800-30719400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:30717800-30719400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:30717800-30719400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:30717800-30719400	Active TSS	Brain Hippocampus Middle	brain
6	chr4:30717800-30719600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:30717800-30719600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:30717800-30719600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:30717800-30719600	Active TSS	Fetal Muscle Leg	muscle
10	chr4:30717800-30719600	Active TSS	HMEC	breast
11	chr4:30717800-30719600	Active TSS	NH-A	brain
12	chr4:30717800-30719800	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr4:30717800-30719800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr4:30717800-30719800	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr4:30717800-30720200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr4:30717800-30720200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:30717800-30720200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:30717800-30720200	Active TSS	Hela-S3	cervix
19	chr4:30717800-30720200	Active TSS	NHEK	skin
20	chr4:30717800-30720400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:30717800-30723000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:30717800-30723000	Active TSS	Right Ventricle	heart
23	chr4:30717800-30723000	Active TSS	Stomach Smooth Muscle	stomach
24	chr4:30717800-30723800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:30717800-30723800	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr4:30717800-30724200	Active TSS	Aorta	Aorta
27	chr4:30717800-30724200	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr4:30717800-30724200	Active TSS	Brain Substantia Nigra	brain
29	chr4:30717800-30724600	Active TSS	Fetal Brain Female	brain
30	chr4:30717800-30725000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:30717800-30726600	Active TSS	Brain Anterior Caudate	brain
32	chr4:30717800-30728200	Active TSS	Brain Angular Gyrus	brain
33	chr4:30717800-30728200	Active TSS	Colon Smooth Muscle	Colon
34	chr4:30717800-30728400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:30718000-30719400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr4:30718000-30719800	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr4:30718000-30720000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:30718000-30720400	Active TSS	Fetal Stomach	stomach
39	chr4:30718000-30720600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:30718000-30721800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:30718000-30723200	Active TSS	NHDF-Ad	bronchial
42	chr4:30718000-30723800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:30718000-30724000	Active TSS	Ovary	ovary
44	chr4:30718000-30724200	Active TSS	NHLF	lung
45	chr4:30718000-30726200	Active TSS	Left Ventricle	heart
46	chr4:30718000-30726600	Active TSS	Brain Cingulate Gyrus	brain
47	chr4:30718200-30719400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:30718200-30719800	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr4:30718200-30723200	Active TSS	Rectal Smooth Muscle	rectum
50	chr4:30718200-30724200	Active TSS	Fetal Kidney	kidney

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