Variant report

Variant	esv3366612
Chromosome Location	chr4:1221130-1221582
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	CTCF	chr4:1221264-1221330	GM19239	blood:	n/a	n/a
2	CTCF	chr4:1221267-1221395	GM12891	blood:	n/a	n/a
3	CTCF	chr4:1221088-1221233	GM19239	blood:	n/a	n/a
4	CTCF	chr4:1221172-1221251	GM12891	blood:	n/a	n/a
5	MAFK	chr4:1221415-1221521	HepG2	liver:	n/a	n/a
6	MAX	chr4:1220862-1221170	NB4	blood:	n/a	chr4:1221049-1221059 chr4:1221020-1221030
7	MYC	chr4:1221285-1221310	MCF-7	breast:	n/a	n/a
8	MYC	chr4:1221062-1221156	GM12878	blood:	n/a	n/a
9	NR2C2	chr4:1221000-1221621	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:1220969-1221659	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr4:1221402-1221403	MCF-7	breast:	n/a	n/a
12	POLR2A	chr4:1220991-1221558	A549	lung:	n/a	n/a
13	POLR2A	chr4:1220832-1221542	HepG2	liver:	n/a	n/a
14	POLR2A	chr4:1221045-1221632	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr4:1220840-1221676	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:1221408-1221438	MCF-7	breast:	n/a	n/a
17	POLR2A	chr4:1221549-1221557	MCF-7	breast:	n/a	n/a
18	POLR2A	chr4:1220947-1221665	GM12891	blood:	n/a	n/a
19	POLR2A	chr4:1220811-1221679	GM12878	blood:	n/a	n/a
20	POLR2A	chr4:1221044-1221266	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr4:1221083-1221341	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr4:1221224-1221826	PFSK-1	brain:	n/a	n/a
23	POLR2A	chr4:1220899-1221677	A549	lung:	n/a	n/a
24	POLR2A	chr4:1221334-1222064	HL-60	blood:	n/a	n/a
25	POLR2A	chr4:1220197-1221945	HepG2	liver:	n/a	n/a
26	POLR2A	chr4:1220846-1221375	HepG2	liver:	n/a	n/a
27	POLR2A	chr4:1221277-1221638	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:1220918-1221616	MCF-7	breast:	n/a	n/a
29	POLR2A	chr4:1221163-1222120	HL-60	blood:	n/a	n/a
30	POLR2A	chr4:1220813-1221604	GM12892	blood:	n/a	n/a
31	POLR2A	chr4:1220310-1224704	K562	blood:	n/a	n/a
32	POLR2A	chr4:1220852-1221607	GM12891	blood:	n/a	n/a
33	POLR2A	chr4:1221160-1221401	MCF-7	breast:	n/a	n/a
34	POLR2A	chr4:1220858-1221532	K562	blood:	n/a	n/a
35	POLR2A	chr4:1220715-1221835	GM12892	blood:	n/a	n/a
36	POLR2A	chr4:1221137-1221425	ProgFib	skin:	n/a	n/a
37	POLR2A	chr4:1220876-1221173	K562	blood:	n/a	n/a
38	POLR2A	chr4:1221098-1221540	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr4:1221022-1221595	A549	lung:	n/a	n/a
40	POLR2A	chr4:1221441-1221514	MCF-7	breast:	n/a	n/a
41	POLR2A	chr4:1220801-1221728	GM12878	blood:	n/a	n/a
42	POLR2A	chr4:1221218-1221401	MCF-7	breast:	n/a	n/a
43	POLR2A	chr4:1221084-1221283	U87	brain:	n/a	n/a
44	POLR2A	chr4:1221537-1221726	K562	blood:	n/a	n/a
45	POLR2A	chr4:1220807-1221663	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr4:1221338-1221736	U87	brain:	n/a	n/a
47	POLR2A	chr4:1221270-1221541	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr4:1220989-1221654	A549	lung:	n/a	n/a
49	SPI1	chr4:1221505-1222094	HL-60	blood:	n/a	chr4:1221777-1221790 chr4:1221778-1221791 chr4:1221781-1221788
50	SPI1	chr4:1221536-1221977	HL-60	blood:	n/a	chr4:1221777-1221790 chr4:1221778-1221791 chr4:1221781-1221788

No.	Distal block	Cell Line	Cell type
1	chr4:1216435..1221821-chr4:1240439..1244617,5	MCF-7	breast:
2	chr4:1215883..1221793-chr4:1233494..1238232,6	K562	blood:
3	chr4:1219143..1221497-chr4:1224349..1226849,2	MCF-7	breast:
4	chr4:1195937..1198894-chr4:1221468..1224458,3	K562	blood:
5	chr4:1218830..1221524-chr4:1242783..1244802,2	MCF-7	breast:

Variant related genes	Relation type
CTBP1	TF binding region
ENSG00000159692	chromatin interactions
ENSG00000196810	chromatin interactions
ENSG00000159674	chromatin interactions

Extended variants
information (count: 38 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1680054	chr4:1221136-1221137	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs544690136	chr4:1221174-1221175	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs563073261	chr4:1221189-1221190	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs370471339	chr4:1221194-1221195	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs142472619	chr4:1221195-1221196	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs1680053	chr4:1221201-1221202	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs375154404	chr4:1221211-1221212	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs529588393	chr4:1221231-1221232	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs547815146	chr4:1221232-1221233	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs201575592	chr4:1221243-1221244	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs372899203	chr4:1221265-1221266	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs552589812	chr4:1221281-1221282	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs79315837	chr4:1221287-1221288	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs570128145	chr4:1221288-1221289	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs537548151	chr4:1221304-1221305	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs2046152	chr4:1221331-1221332	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	mRNA abundance
17	rs567602468	chr4:1221359-1221360	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs534911471	chr4:1221375-1221376	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs374507125	chr4:1221380-1221381	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs377572342	chr4:1221396-1221397	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs370138006	chr4:1221400-1221401	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs374458962	chr4:1221406-1221407	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs2046151	chr4:1221441-1221442	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs574954429	chr4:1221450-1221451	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs371865573	chr4:1221459-1221460	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs376788665	chr4:1221460-1221461	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs191789485	chr4:1221475-1221476	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs115837454	chr4:1221487-1221488	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs528106895	chr4:1221490-1221491	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs541688048	chr4:1221492-1221493	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs559765815	chr4:1221499-1221500	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs533681194	chr4:1221509-1221510	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs572985829	chr4:1221535-1221536	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs536442909	chr4:1221542-1221543	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs554496085	chr4:1221543-1221544	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs138627323	chr4:1221560-1221561	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
37	rs570264023	chr4:1221564-1221565	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs531026181	chr4:1221566-1221567	Strong transcription ZNF genes & repeats Genic enhancers Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	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
small cell lung cancer	20016488	CNVD
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	20932292	CNVD
Pancreatic cancer	17952125	CNVD
Type 2 diabetes	21754918	CNVD
Breast cancer	22522925	CNVD
Breast cancer	20393555	CNVD

Chromatin state (count:135 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1203800-1223000	Strong transcription	Osteobl	bone
2	chr4:1204400-1227200	Strong transcription	Fetal Intestine Small	intestine
3	chr4:1204400-1235800	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr4:1204600-1236200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:1204800-1226400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:1204800-1237000	Weak transcription	Psoas Muscle	Psoas
7	chr4:1205000-1226200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:1205400-1226800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:1205800-1228200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:1206000-1226800	Strong transcription	Fetal Brain Female	brain
11	chr4:1206400-1226800	Strong transcription	Brain Germinal Matrix	brain
12	chr4:1206600-1227600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:1208800-1228000	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr4:1210600-1225200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:1211400-1235400	Weak transcription	Small Intestine	intestine
16	chr4:1211600-1235400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:1212600-1225200	Strong transcription	Fetal Muscle Leg	muscle
18	chr4:1212600-1237000	Strong transcription	Dnd41	blood
19	chr4:1213600-1224200	Strong transcription	Placenta	Placenta
20	chr4:1213800-1221800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:1214200-1221200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr4:1214200-1221600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:1214200-1235600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr4:1214200-1236800	Strong transcription	Primary T cells from cord blood	blood
25	chr4:1214400-1222200	Strong transcription	Brain Cingulate Gyrus	brain
26	chr4:1214400-1222200	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr4:1214400-1225000	Strong transcription	Brain Hippocampus Middle	brain
28	chr4:1214400-1225600	Strong transcription	Aorta	Aorta
29	chr4:1214400-1235200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:1214400-1235600	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr4:1214400-1236400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr4:1214400-1238400	Strong transcription	Thymus	Thymus
33	chr4:1214600-1225400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:1214600-1226400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr4:1214600-1227400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:1214600-1227600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:1214600-1235800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:1214600-1236200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:1215000-1226800	Strong transcription	Colonic Mucosa	Colon
40	chr4:1215000-1235200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:1215000-1236000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr4:1215400-1225800	Strong transcription	Brain Anterior Caudate	brain
43	chr4:1215400-1226600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:1215400-1236000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr4:1215800-1226600	Strong transcription	Fetal Stomach	stomach
46	chr4:1215800-1235600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:1216400-1227800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:1216400-1227800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr4:1216400-1235400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:1216400-1236000	Strong transcription	Fetal Thymus	thymus

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