Variant report

Variant	esv1815732
Chromosome Location	chr19:23560602-23568319
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	chr19:23566240-23566390	GM12866	blood:	n/a	n/a
2	JUND	chr19:23561672-23561941	HepG2	liver:	n/a	chr19:23561805-23561817 chr19:23561807-23561815 chr19:23561806-23561815 chr19:23561805-23561816 chr19:23561806-23561816 chr19:23561807-23561814
3	KAP1	chr19:23561682-23562033	U2OS	brain:	n/a	chr19:23561805-23561814
4	MYC	chr19:23567847-23567873	MCF-7	breast:	n/a	n/a
5	MYC	chr19:23567891-23567921	MCF-7	breast:	n/a	n/a
6	MYC	chr19:23567875-23567876	MCF-7	breast:	n/a	n/a
7	POLR2A	chr19:23567831-23567844	MCF-7	breast:	n/a	n/a
8	POLR2A	chr19:23562617-23562627	A549	lung:	n/a	n/a
9	POLR2A	chr19:23562610-23562841	Gliobla	brain:	n/a	n/a
10	POLR2A	chr19:23567846-23567850	A549	lung:	n/a	n/a
11	POLR2A	chr19:23566060-23566143	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:23566796-23566894	ProgFib	skin:	n/a	n/a
13	POLR2A	chr19:23567875-23567938	A549	lung:	n/a	n/a
14	POLR2A	chr19:23567829-23567830	MCF-7	breast:	n/a	n/a
15	POLR2A	chr19:23562676-23562704	MCF-7	breast:	n/a	n/a
16	POLR2A	chr19:23562272-23562457	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:23565108-23565308	MCF10A-Er-Src	breast:	n/a	n/a
18	RFX5	chr19:23565735-23565820	K562	blood:	n/a	n/a
19	SETDB1	chr19:23565665-23566174	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:23564648..23566828-chr19:23577196..23579466,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF730-13	chr19:23567332-23568095	NONHSAT063905
2	lnc-ZNF730-12	chr19:23563119-23563678	NONHSAT063904

Variant related genes	Relation type
ENSG00000268992	TF binding region
ENSG00000269431	TF binding region
ENSG00000167232	chromatin interactions

Extended variants
information (count: 296 )
Associated
traits (count: 40 )

Variant overlapped rSNPs/rCNVs (count:296 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536854267	chr19:23560602-23560603	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs55812273	chr19:23560624-23560625	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs140844489	chr19:23560647-23560648	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs372969467	chr19:23560650-23560651	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs573617696	chr19:23560653-23560654	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs183077526	chr19:23560733-23560734	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs150005884	chr19:23560741-23560742	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs546934022	chr19:23560750-23560751	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs200346310	chr19:23560756-23560757	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs35876084	chr19:23560757-23560758	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs113921867	chr19:23560758-23560759	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs145273120	chr19:23560786-23560787	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs544674155	chr19:23560813-23560814	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs571143703	chr19:23560890-23560891	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs563372595	chr19:23560920-23560921	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs533483226	chr19:23560930-23560931	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs543257439	chr19:23560940-23560941	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs561439100	chr19:23560958-23560959	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs538585485	chr19:23560986-23560987	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs185916824	chr19:23561069-23561070	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs547306131	chr19:23561106-23561107	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs59863959	chr19:23561185-23561186	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs532586277	chr19:23561192-23561193	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs550515956	chr19:23561210-23561211	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs569021063	chr19:23561233-23561234	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs530102505	chr19:23561245-23561246	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs548790358	chr19:23561371-23561372	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs370698932	chr19:23561400-23561401	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs374085226	chr19:23561409-23561410	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs567154997	chr19:23561440-23561441	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs538915225	chr19:23561453-23561454	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs73565049	chr19:23561466-23561467	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs367933288	chr19:23561472-23561473	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs566991936	chr19:23561475-23561476	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs553277978	chr19:23561496-23561497	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs536051889	chr19:23561513-23561514	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs35913751	chr19:23561531-23561532	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs73565050	chr19:23561556-23561557	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs141861411	chr19:23561563-23561564	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs377469175	chr19:23561590-23561591	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs370329066	chr19:23561616-23561617	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs575433312	chr19:23561620-23561621	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs542771828	chr19:23561629-23561630	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs73565051	chr19:23561712-23561713	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs573424415	chr19:23561722-23561723	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs199516743	chr19:23561736-23561737	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs150108102	chr19:23561764-23561765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs34139256	chr19:23561804-23561805	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs397814737	chr19:23561805-23561806	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs398101147	chr19:23561806-23561807	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:40)

Disease	PMID	Source
Medulloblastoma	16783165	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Prostate cancer	16573809	CNVD
Chordoma	18071362	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	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
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myelofibrosis	22110671	CNVD
Cancer	21183584	CNVD
Colorectal cancer	20459617	CNVD
Ductal carcinoma	22052326	CNVD
Cancer	20164920	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:508 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23513200-23570400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:23524400-23570200	ZNF genes & repeats	Liver	Liver
3	chr19:23524600-23570000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
4	chr19:23544000-23576400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:23549200-23560800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:23549200-23568600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr19:23549200-23570200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:23549200-23577000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:23549600-23576000	Weak transcription	Hela-S3	cervix
10	chr19:23549800-23562400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:23551600-23576400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:23552200-23562000	Weak transcription	Right Ventricle	heart
13	chr19:23552400-23562600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:23552800-23576000	ZNF genes & repeats	Dnd41	blood
15	chr19:23553000-23560800	ZNF genes & repeats	Fetal Brain Female	brain
16	chr19:23553000-23576400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:23553000-23576800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr19:23553000-23577000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr19:23554200-23567600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:23554800-23562000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr19:23555600-23562200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:23555600-23562600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr19:23555600-23562600	Weak transcription	Psoas Muscle	Psoas
24	chr19:23555600-23576800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:23555800-23561800	Weak transcription	Esophagus	oesophagus
26	chr19:23555800-23562400	Weak transcription	Spleen	Spleen
27	chr19:23555800-23562600	Weak transcription	Gastric	stomach
28	chr19:23556000-23562000	Weak transcription	Brain Angular Gyrus	brain
29	chr19:23556000-23562400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:23556000-23566600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:23556600-23562400	Weak transcription	Pancreas	Pancrea
32	chr19:23556800-23561800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr19:23556800-23561800	Weak transcription	NH-A	brain
34	chr19:23556800-23562400	Weak transcription	Brain Substantia Nigra	brain
35	chr19:23556800-23566000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:23557000-23561800	Weak transcription	Fetal Brain Male	brain
37	chr19:23557000-23561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:23557000-23566200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr19:23557200-23561600	Weak transcription	Colonic Mucosa	Colon
40	chr19:23557200-23576600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:23557800-23563400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr19:23558200-23560800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
43	chr19:23558200-23561200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:23558200-23563000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
45	chr19:23558200-23563200	ZNF genes & repeats	GM12878-XiMat	blood
46	chr19:23558200-23573200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
47	chr19:23558600-23562400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:23558600-23569000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:23558800-23560800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
50	chr19:23558800-23560800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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