Variant report

Variant	esv3505945
Chromosome Location	chr19:18057049-18057199
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	ATF2	chr19:18057032-18057408	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF3	chr19:18057186-18057406	K562	blood:	n/a	n/a
3	ATF3	chr19:18057075-18057454	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr19:18057170-18057408	H1-hESC	embryonic stem cell:	n/a	n/a
5	BCLAF1	chr19:18057078-18057494	GM12878	blood:	n/a	n/a
6	CTCF	chr19:18057165-18057399	LNCaP	prostate:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
7	CTCF	chr19:18057165-18057403	MCF-7	breast:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
8	CTCF	chr19:18057176-18057437	MCF-7	breast:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
9	CTCF	chr19:18057087-18057501	HepG2	liver:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
10	CTCF	chr19:18057172-18057429	H1-hESC	embryonic stem cell:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
11	CTCF	chr19:18057197-18057449	A549	lung:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
12	CTCF	chr19:18057139-18057414	Medullo	brain:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
13	CTCF	chr19:18057181-18057402	ECC-1	luminal epithelium:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
14	CTCF	chr19:18056944-18057084	GM12891	blood:	n/a	n/a
15	CTCF	chr19:18057177-18057373	Kidney_OC	kidney:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
16	CTCF	chr19:18056943-18057481	HCT-116	colon:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
17	CTCF	chr19:18057159-18057415	ProgFib	skin:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
18	CTCF	chr19:18057170-18057414	Pancreas_OC	pancreas:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
19	CTCF	chr19:18057166-18057430	GM19239	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
20	CTCF	chr19:18057007-18057050	GM10248	blood:	n/a	n/a
21	CTCF	chr19:18057180-18057330	HVMF	connective:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
22	CTCF	chr19:18057166-18057405	GM13977	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
23	CTCF	chr19:18057095-18057470	IMR90	lung:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
24	CTCF	chr19:18057152-18057426	GM10266	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
25	CTCF	chr19:18057160-18057310	HL-60	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
26	CTCF	chr19:18057114-18057421	Spleen_OC	spleen:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
27	CTCF	chr19:18057180-18057330	GM12873	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
28	CTCF	chr19:18057139-18057582	K562	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
29	CTCF	chr19:18057061-18057462	H1-hESC	embryonic stem cell:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
30	CTCF	chr19:18057138-18057435	Gliobla	brain:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
31	CTCF	chr19:18057138-18057420	HUVEC	blood vessel:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
32	CTCF	chr19:18056926-18057063	GM12892	blood:	n/a	n/a
33	CTCF	chr19:18057007-18057468	MCF-7	breast:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
34	CTCF	chr19:18056959-18057080	GM19239	blood:	n/a	n/a
35	CTCF	chr19:18057183-18057396	A549	lung:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
36	CTCF	chr19:18057100-18057250	GM12873	blood:	n/a	n/a
37	CTCF	chr19:18057140-18057290	HA-sp	spinal cord:	n/a	n/a
38	CTCF	chr19:18057145-18057430	Hela-S3	cervix:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
39	CTCF	chr19:18057143-18057411	A549	lung:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
40	CTCF	chr19:18057174-18057421	LNCaP	prostate:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
41	CTCF	chr19:18057180-18057330	HPF	lung:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
42	CTCF	chr19:18057180-18057330	GM12867	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
43	CTCF	chr19:18057180-18057330	GM12864	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
44	CTCF	chr19:18057140-18057290	HCM	heart:	n/a	n/a
45	CTCF	chr19:18056936-18057076	GM19238	blood:	n/a	n/a
46	CTCF	chr19:18056908-18057486	A549	lung:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
47	CTCF	chr19:18057127-18057424	GM12878	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
48	CTCF	chr19:18057152-18057411	T-47D	breast:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
49	CTCF	chr19:18056636-18057547	SK-N-SH	brain:	n/a	chr19:18057281-18057299 chr19:18057284-18057297
50	CTCF	chr19:18057155-18057414	GM10248	blood:	n/a	chr19:18057281-18057299 chr19:18057284-18057297

No.	Distal block	Cell Line	Cell type
1	chr19:18056861..18058558-chr19:18107372..18108294,7	K562	blood:
2	chr19:17969435..17972591-chr19:18056494..18062279,6	K562	blood:
3	chr19:18049354..18052020-chr19:18056652..18058961,3	MCF-7	breast:
4	chr19:18055988..18065489-chr19:18073307..18083163,16	K562	blood:
5	chr19:18057090..18059767-chr19:18110634..18113948,3	MCF-7	breast:
6	chr19:17984874..17987363-chr19:18056604..18058812,2	K562	blood:
7	chr19:18055450..18057221-chr19:18107817..18109855,2	MCF-7	breast:
8	chr19:18051562..18057273-chr19:18105982..18113371,17	K562	blood:
9	chr19:18052069..18059812-chr19:18106129..18113779,16	K562	blood:
10	chr19:18056470..18058244-chr19:18107377..18108277,8	MCF-7	breast:
11	chr19:18057024..18060346-chr19:18095045..18097691,3	K562	blood:

Variant related genes	Relation type
KCNN1	TF binding region
ENSG00000105640	chromatin interactions
ENSG00000105642	chromatin interactions
ENSG00000105643	chromatin interactions
ENSG00000252591	chromatin interactions

Extended variants
information (count: 5 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs111879493	chr19:18057070-18057071	Weak transcription Enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs11086085	chr19:18057087-18057088	Weak transcription Enhancers Active TSS	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs532585217	chr19:18057094-18057095	Weak transcription Enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs552711428	chr19:18057110-18057111	Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs566130269	chr19:18057168-18057169	Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Medulloblastoma	16783165	CNVD
Follicular lymphoma	20505157	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-syndromic sensorineural hearing loss	20179077	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21080181	CNVD
Metanephric adenoma	20802469	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Lung cancer	17297452	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Chordoma	18071362	CNVD
Ewing''s sarcoma	21437220	CNVD
Medulloblastoma	21979893	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
ovarian endometriomas	16273235	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Cervical cancer	21063398	CNVD
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Ovarian cancer	21720365	CNVD
Urothelial carcinoma	21177765	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Basal cell lymphoma	21115979	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Breast cancer	21364760	CNVD
Mycobacterial infection	18421352	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute monocytic leukemia	16498392	CNVD
Lung cancer	18438408	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Liver carcinoma	19366792	CNVD
Colorectal cancer	19455253	CNVD
Lujan-Fryns syndrom	21521776	CNVD
Breast cancer	20409316	CNVD
Cancer	17160897	CNVD
Cancer	17440070	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	21509527	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18044600-18058200	Weak transcription	Psoas Muscle	Psoas
2	chr19:18044800-18057800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:18044800-18057800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:18044800-18058000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:18044800-18058000	Weak transcription	Fetal Brain Male	brain
6	chr19:18044800-18058000	Weak transcription	Fetal Kidney	kidney
7	chr19:18044800-18058000	Weak transcription	Small Intestine	intestine
8	chr19:18044800-18058200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:18045000-18057800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:18045000-18057800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr19:18045000-18058000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:18045000-18058000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:18045000-18058000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr19:18045000-18058000	Weak transcription	Fetal Heart	heart
15	chr19:18045000-18058000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:18045200-18058000	Weak transcription	Stomach Mucosa	stomach
17	chr19:18047800-18058200	Weak transcription	Left Ventricle	heart
18	chr19:18048600-18058000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:18051200-18058000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:18051200-18058000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:18051200-18058200	Weak transcription	Aorta	Aorta
22	chr19:18051400-18057600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr19:18051400-18058000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:18051400-18058000	Weak transcription	Brain Anterior Caudate	brain
25	chr19:18051400-18058000	Weak transcription	Brain Substantia Nigra	brain
26	chr19:18052000-18057200	Weak transcription	Fetal Thymus	thymus
27	chr19:18052800-18057600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr19:18052800-18058000	Weak transcription	Brain Angular Gyrus	brain
29	chr19:18053000-18058000	Weak transcription	Pancreas	Pancrea
30	chr19:18053000-18058000	Weak transcription	Hela-S3	cervix
31	chr19:18053200-18058000	Weak transcription	Liver	Liver
32	chr19:18053600-18058000	Weak transcription	Fetal Intestine Large	intestine
33	chr19:18053800-18058000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr19:18054000-18057800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr19:18054000-18058000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:18054000-18058000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr19:18054000-18058000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr19:18054200-18058000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:18054200-18058200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:18054600-18057800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:18054600-18058000	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:18054600-18058000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr19:18054800-18057800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:18054800-18058000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:18054800-18058200	Weak transcription	Fetal Lung	lung
46	chr19:18055000-18057200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr19:18055000-18057800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:18055000-18057800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:18055000-18057800	Weak transcription	Colonic Mucosa	Colon
50	chr19:18055000-18057800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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