Variant report

Variant	esv3392236
Chromosome Location	chr19:18552871-18552984
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	BHLHE40	chr19:18552909-18552926	GM12878	blood:	n/a	n/a
2	BHLHE40	chr19:18552765-18552888	K562	blood:	n/a	n/a
3	CBX3	chr19:18552322-18553236	K562	blood:	n/a	n/a
4	CBX3	chr19:18552735-18553015	K562	blood:	n/a	n/a
5	CTCF	chr19:18552784-18553111	GM19239	blood:	n/a	n/a
6	EGR1	chr19:18552448-18553531	K562	blood:	n/a	chr19:18552562-18552572 chr19:18552568-18552581 chr19:18552567-18552582 chr19:18552569-18552578 chr19:18552573-18552583 chr19:18552568-18552581 chr19:18552562-18552575
7	EGR1	chr19:18552725-18552898	GM12878	blood:	n/a	n/a
8	EGR1	chr19:18552396-18553538	K562	blood:	n/a	chr19:18552562-18552572 chr19:18552568-18552581 chr19:18552567-18552582 chr19:18552569-18552578 chr19:18552573-18552583 chr19:18552568-18552581 chr19:18552562-18552575
9	FOSL2	chr19:18549286-18553091	HepG2	liver:	n/a	n/a
10	GABPA	chr19:18552420-18553109	K562	blood:	n/a	n/a
11	GATA2	chr19:18552448-18552894	K562	blood:	n/a	chr19:18552656-18552673 chr19:18552655-18552662 chr19:18552654-18552664 chr19:18552655-18552662 chr19:18552655-18552662 chr19:18552653-18552665
12	HCFC1	chr19:18552975-18552999	K562	blood:	n/a	n/a
13	MAX	chr19:18552330-18553032	K562	blood:	n/a	n/a
14	MAZ	chr19:18552566-18553013	K562	blood:	n/a	n/a
15	MTA3	chr19:18552714-18553097	GM12878	blood:	n/a	n/a
16	MYC	chr19:18552738-18553156	MCF-7	breast:	n/a	n/a
17	MYC	chr19:18552812-18553088	MCF-7	breast:	n/a	n/a
18	NFATC1	chr19:18552492-18553198	GM12878	blood:	n/a	n/a
19	NFATC1	chr19:18552691-18552982	GM12878	blood:	n/a	n/a
20	NR2F2	chr19:18552468-18553018	K562	blood:	n/a	n/a
21	NR2F2	chr19:18552365-18553002	K562	blood:	n/a	n/a
22	PML	chr19:18552482-18553005	K562	blood:	n/a	n/a
23	POLR2A	chr19:18552728-18553232	MCF-7	breast:	n/a	n/a
24	POLR2A	chr19:18552624-18552997	K562	blood:	n/a	n/a
25	POLR2A	chr19:18552796-18553464	HepG2	liver:	n/a	n/a
26	POLR2A	chr19:18552234-18553014	K562	blood:	n/a	n/a
27	POLR2A	chr19:18552724-18553219	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:18552651-18553364	GM12892	blood:	n/a	n/a
29	POLR2A	chr19:18534926-18553479	K562	blood:	n/a	n/a
30	POLR2A	chr19:18552885-18552906	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr19:18552732-18553253	MCF-7	breast:	n/a	n/a
32	POLR2A	chr19:18552627-18553369	GM12891	blood:	n/a	n/a
33	POLR2A	chr19:18552847-18553084	MCF-7	breast:	n/a	n/a
34	POLR2A	chr19:18552793-18553343	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:18552705-18553231	GM12891	blood:	n/a	n/a
36	POLR2A	chr19:18550683-18553505	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:18550619-18553582	HepG2	liver:	n/a	n/a
38	POLR2A	chr19:18552675-18553464	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:18552780-18553401	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:18552870-18553434	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:18550978-18553248	GM12892	blood:	n/a	n/a
42	POLR2A	chr19:18552905-18553076	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr19:18550597-18553492	GM12892	blood:	n/a	n/a
44	POLR2A	chr19:18552646-18553306	GM12891	blood:	n/a	n/a
45	POLR2A	chr19:18552863-18553379	K562	blood:	n/a	n/a
46	POLR2A	chr19:18552861-18553072	K562	blood:	n/a	n/a
47	RCOR1	chr19:18552354-18552934	K562	blood:	n/a	n/a
48	RCOR1	chr19:18552371-18552932	K562	blood:	n/a	n/a
49	RUNX3	chr19:18552541-18553420	GM12878	blood:	n/a	chr19:18553012-18553027 chr19:18552981-18552996
50	RUNX3	chr19:18552582-18553507	GM12878	blood:	n/a	chr19:18553012-18553027 chr19:18552981-18552996

No.	Distal block	Cell Line	Cell type
1	chr19:18495925..18498880-chr19:18550697..18553844,3	K562	blood:
2	chr19:18552236..18554463-chr19:18572240..18574871,2	K562	blood:
3	chr19:18552619..18554243-chr19:18681800..18683781,2	K562	blood:

Variant related genes	Relation type
ISYNA1	TF binding region
ENSG00000264175	chromatin interactions
ENSG00000221983	chromatin interactions
ENSG00000130513	chromatin interactions

Extended variants
information (count: 11 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs202046992	chr19:18552882-18552883	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs200023260	chr19:18552906-18552907	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs201618648	chr19:18552909-18552910	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs199626630	chr19:18552914-18552915	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs371049315	chr19:18552917-18552918	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs200498684	chr19:18552919-18552920	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs200895868	chr19:18552936-18552937	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs73523092	chr19:18552961-18552962	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs201920710	chr19:18552974-18552975	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs199748639	chr19:18552975-18552976	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs372271725	chr19:18552977-18552978	Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

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

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18545200-18570000	Weak transcription	Small Intestine	intestine
2	chr19:18548600-18554200	Weak transcription	Dnd41	blood
3	chr19:18548800-18553200	Weak transcription	Fetal Kidney	kidney
4	chr19:18548800-18554200	Weak transcription	NHDF-Ad	bronchial
5	chr19:18549200-18554200	Enhancers	Placenta	Placenta
6	chr19:18549200-18554400	Weak transcription	Primary B cells from cord blood	blood
7	chr19:18549200-18559600	Weak transcription	HSMM	muscle
8	chr19:18549200-18566200	Weak transcription	HUVEC	blood vessel
9	chr19:18549400-18553400	Enhancers	Fetal Intestine Large	intestine
10	chr19:18549400-18554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:18549400-18554600	Weak transcription	Brain Angular Gyrus	brain
12	chr19:18549400-18556400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:18549600-18553000	Weak transcription	Brain Anterior Caudate	brain
14	chr19:18549600-18553000	Weak transcription	Gastric	stomach
15	chr19:18549600-18553400	Enhancers	Fetal Intestine Small	intestine
16	chr19:18549600-18553400	Enhancers	Pancreas	Pancrea
17	chr19:18549600-18554000	Weak transcription	Brain Germinal Matrix	brain
18	chr19:18549600-18554200	Weak transcription	Brain Substantia Nigra	brain
19	chr19:18549600-18554400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:18549600-18554400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr19:18549800-18553200	Weak transcription	Colonic Mucosa	Colon
22	chr19:18549800-18553400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:18549800-18554000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:18549800-18554200	Weak transcription	Fetal Brain Female	brain
25	chr19:18549800-18554600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:18549800-18567000	Weak transcription	Psoas Muscle	Psoas
27	chr19:18550000-18553800	Weak transcription	Left Ventricle	heart
28	chr19:18550000-18553800	Weak transcription	Right Ventricle	heart
29	chr19:18550000-18553800	Weak transcription	Thymus	Thymus
30	chr19:18550000-18554000	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:18550000-18554200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:18550000-18554400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:18550000-18554400	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:18550200-18553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr19:18550200-18554400	Weak transcription	Adipose Nuclei	Adipose
36	chr19:18550200-18554600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr19:18550200-18559600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr19:18550400-18553800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:18550400-18554000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:18550400-18554400	Weak transcription	Aorta	Aorta
41	chr19:18550400-18554400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:18550400-18557200	Weak transcription	Fetal Lung	lung
43	chr19:18550600-18553000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:18550600-18553000	Weak transcription	Esophagus	oesophagus
45	chr19:18550600-18553600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr19:18550600-18553800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr19:18550600-18553800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr19:18550600-18554600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:18550600-18554600	Weak transcription	Osteobl	bone
50	chr19:18550600-18562000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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