Variant report

Variant	esv3468255
Chromosome Location	chr4:78237484-78277631
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	chr4:78268651-78268718	HepG2	liver:	n/a	n/a
2	ATF1	chr4:78267547-78267723	K562	blood:	n/a	n/a
3	BHLHE40	chr4:78265976-78266449	GM12878	blood:	n/a	n/a
4	CBX3	chr4:78263269-78263765	HCT-116	colon:	n/a	n/a
5	CBX3	chr4:78253746-78254319	HCT-116	colon:	n/a	n/a
6	CBX3	chr4:78253824-78254202	K562	blood:	n/a	n/a
7	CBX3	chr4:78253883-78254139	K562	blood:	n/a	n/a
8	CBX3	chr4:78263352-78263680	HCT-116	colon:	n/a	n/a
9	CBX3	chr4:78263330-78263629	K562	blood:	n/a	n/a
10	CEBPB	chr4:78268366-78268440	K562	blood:	n/a	chr4:78268368-78268377 chr4:78268366-78268379 chr4:78268368-78268379
11	CEBPB	chr4:78268252-78268595	HepG2	liver:	n/a	chr4:78268368-78268377 chr4:78268366-78268379 chr4:78268368-78268379
12	CEBPB	chr4:78268359-78268485	IMR90	lung:	n/a	chr4:78268368-78268377 chr4:78268366-78268379 chr4:78268368-78268379
13	CHD2	chr4:78254095-78254505	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr4:78274860-78275010	GM06990	blood:	n/a	n/a
15	CTCF	chr4:78274800-78274950	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr4:78274840-78274990	NHLF	lung:	n/a	n/a
17	CTCF	chr4:78274860-78275010	WERI-Rb-1	eye:	n/a	n/a
18	CTCF	chr4:78274860-78275010	SAEC	small airway:	n/a	n/a
19	CTCF	chr4:78274860-78275010	HEEpiC	esophagus:	n/a	n/a
20	CTCF	chr4:78274860-78275010	HUVEC	blood vessel:	n/a	n/a
21	CTCF	chr4:78275260-78275410	GM12872	blood:	n/a	n/a
22	CTCF	chr4:78275220-78275370	NHDF-neo	bronchial:	n/a	n/a
23	CTCF	chr4:78275240-78275390	AG09309	skin:	n/a	n/a
24	CTCF	chr4:78274860-78275010	GM12874	blood:	n/a	n/a
25	CTCF	chr4:78274860-78275010	GM12868	blood:	n/a	n/a
26	CTCF	chr4:78274840-78274990	HCM	heart:	n/a	n/a
27	CTCF	chr4:78274840-78274990	HCT-116	colon:	n/a	n/a
28	CTCF	chr4:78274860-78275010	HRE	kidney:	n/a	n/a
29	CTCF	chr4:78274320-78274470	GM12870	blood:	n/a	n/a
30	CTCF	chr4:78274840-78274990	HCFaa	heart:	n/a	n/a
31	CTCF	chr4:78274979-78275265	Pancreas_OC	pancreas:	n/a	chr4:78275103-78275121 chr4:78275105-78275126 chr4:78275106-78275119
32	CTCF	chr4:78274640-78274790	HCM	heart:	n/a	n/a
33	CTCF	chr4:78274948-78275275	ProgFib	skin:	n/a	chr4:78275103-78275121 chr4:78275105-78275126 chr4:78275106-78275119
34	CTCF	chr4:78274860-78275010	NB4	blood:	n/a	n/a
35	CTCF	chr4:78274981-78275241	GM13976	blood:	n/a	chr4:78275103-78275121 chr4:78275105-78275126 chr4:78275106-78275119
36	CTCF	chr4:78274860-78275010	HMF	breast:	n/a	n/a
37	CTCF	chr4:78274949-78275303	LNCaP	prostate:	n/a	chr4:78275103-78275121 chr4:78275105-78275126 chr4:78275106-78275119
38	CTCF	chr4:78274840-78274990	GM12871	blood:	n/a	n/a
39	CTCF	chr4:78274870-78275069	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr4:78274860-78275010	HMEC	breast:	n/a	n/a
41	CTCF	chr4:78274946-78275271	NHEK	skin:	n/a	chr4:78275103-78275121 chr4:78275105-78275126 chr4:78275106-78275119
42	CTCF	chr4:78275200-78275350	GM12872	blood:	n/a	n/a
43	CTCF	chr4:78274840-78274990	RPTEC	kidney:	n/a	n/a
44	CTCF	chr4:78274969-78275267	HUVEC	blood vessel:	n/a	chr4:78275103-78275121 chr4:78275105-78275126 chr4:78275106-78275119
45	CTCF	chr4:78274860-78275010	HEK293	kidney:	n/a	n/a
46	CTCF	chr4:78274540-78274690	GM12870	blood:	n/a	n/a
47	CTCF	chr4:78274820-78274970	AG04450	lung:	n/a	n/a
48	CTCF	chr4:78274840-78274990	GM12873	blood:	n/a	n/a
49	CTCF	chr4:78274756-78274788	Kidney_OC	kidney:	n/a	n/a
50	CTCF	chr4:78274860-78275010	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:78257188..78259774-chr4:78266144..78268332,2	K562	blood:
2	chr4:78266632..78268344-chr4:78268869..78271315,2	K562	blood:
3	chr4:78270382..78272050-chr4:78274178..78276131,2	K562	blood:
4	chr4:78236163..78238480-chr4:78287943..78289669,2	K562	blood:
5	chr4:78266632..78268344-chr4:78268869..78271315,2	K562	blood:
6	chr4:78257188..78259774-chr4:78266144..78268332,2	K562	blood:
7	chr4:78270382..78272050-chr4:78274178..78276131,2	K562	blood:
8	chr4:78269918..78271823-chr4:78272380..78274841,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNI-6	chr4:78271523-78272388	NONHSAT097053

Variant related genes	Relation type
ENSG00000248831	TF binding region
ENSG00000250006	TF binding region
ENSG00000248831	chromatin interactions

Extended variants
information (count: 2092 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:2092 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs62303626	chr4:78237485-78237486	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs190874271	chr4:78237490-78237491	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs563973771	chr4:78237509-78237510	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs544853597	chr4:78237521-78237522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs564717450	chr4:78237543-78237544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs576357791	chr4:78237557-78237558	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs78216768	chr4:78237569-78237570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs563642647	chr4:78237589-78237590	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs386451745	chr4:78237591-78237592	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs529241277	chr4:78237595-78237596	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs374961484	chr4:78237664-78237665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs566330598	chr4:78237682-78237683	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs143478235	chr4:78237702-78237703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs182537775	chr4:78237736-78237737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs571914018	chr4:78237737-78237738	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs539529132	chr4:78237746-78237747	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs4859486	chr4:78237776-78237777	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs569653146	chr4:78237806-78237807	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs372469236	chr4:78237847-78237848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs386676329	chr4:78237849-78237850	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs370295778	chr4:78237851-78237852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs559167255	chr4:78237852-78237853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs535399862	chr4:78237856-78237857	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs35098730	chr4:78237858-78237859	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs555084315	chr4:78237866-78237867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs572287971	chr4:78237899-78237900	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs540975029	chr4:78237911-78237912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs115023592	chr4:78237927-78237928	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs148012683	chr4:78237931-78237932	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs141695877	chr4:78237945-78237946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs4859487	chr4:78237955-78237956	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs4859488	chr4:78237977-78237978	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs542995608	chr4:78237979-78237980	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs78248357	chr4:78238000-78238001	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs4859489	chr4:78238031-78238032	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs563256693	chr4:78238060-78238061	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs528592095	chr4:78238085-78238086	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs4859801	chr4:78238100-78238101	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs375547451	chr4:78238107-78238108	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs571977660	chr4:78238124-78238125	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs111814614	chr4:78238138-78238139	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs550914311	chr4:78238157-78238158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs114402204	chr4:78238285-78238286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs12651366	chr4:78238290-78238291	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs555320095	chr4:78238402-78238403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs10003077	chr4:78238410-78238411	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs534327099	chr4:78238425-78238426	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs9991635	chr4:78238517-78238518	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs566213364	chr4:78238522-78238523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs567152178	chr4:78238588-78238589	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:74)

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
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
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
Myelofibrosis	22110671	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78233200-78240600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:78240600-78241200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:78241200-78251400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:78252800-78254000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:78253400-78254800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr4:78255400-78256400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:78256400-78259000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:78256800-78257000	ZNF genes & repeats	HMEC	breast
9	chr4:78256800-78259200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:78257000-78257400	Weak transcription	HMEC	breast
11	chr4:78257200-78258000	Enhancers	NHEK	skin
12	chr4:78257400-78259200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:78257400-78259200	Enhancers	HMEC	breast
14	chr4:78258000-78258400	Flanking Active TSS	NHEK	skin
15	chr4:78258400-78259200	Enhancers	NHEK	skin
16	chr4:78259000-78263000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:78259200-78263000	Weak transcription	NHEK	skin
18	chr4:78263000-78264400	ZNF genes & repeats	NHEK	skin
19	chr4:78263000-78265000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:78263400-78263800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:78263400-78264000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr4:78264200-78265200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:78264400-78264600	Weak transcription	NHEK	skin
24	chr4:78264600-78264800	Enhancers	NHEK	skin
25	chr4:78264600-78266600	Enhancers	HMEC	breast
26	chr4:78264800-78265000	Flanking Active TSS	NHEK	skin
27	chr4:78264800-78265600	ZNF genes & repeats	GM12878-XiMat	blood
28	chr4:78264800-78266400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:78264800-78266400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:78265000-78265400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:78265000-78266600	Enhancers	NHEK	skin
32	chr4:78265200-78266200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:78265400-78270200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:78265600-78266000	Weak transcription	GM12878-XiMat	blood
35	chr4:78266000-78266400	Enhancers	GM12878-XiMat	blood
36	chr4:78266200-78270000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:78266400-78269400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:78266600-78269800	Weak transcription	HMEC	breast
39	chr4:78267400-78269800	Enhancers	Fetal Intestine Small	intestine
40	chr4:78267400-78270000	Enhancers	Stomach Mucosa	stomach
41	chr4:78267400-78270200	Enhancers	Fetal Intestine Large	intestine
42	chr4:78267600-78268800	Enhancers	Pancreas	Pancrea
43	chr4:78268000-78268400	Enhancers	HepG2	liver
44	chr4:78268200-78269200	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr4:78268400-78268600	Enhancers	Colonic Mucosa	Colon
46	chr4:78268400-78268800	Enhancers	A549	lung
47	chr4:78268400-78268800	Flanking Active TSS	HepG2	liver
48	chr4:78268400-78269000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:78268400-78269000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr4:78268400-78269400	Enhancers	Duodenum Mucosa	Duodenum

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