Variant report

Variant	esv3443479
Chromosome Location	chr19:56191218-56191478
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	CEBPB	chr19:56190915-56191256	IMR90	lung:	n/a	n/a
2	FOS	chr19:56190976-56191337	MCF10A-Er-Src	breast:	n/a	chr19:56191166-56191173 chr19:56191165-56191173
3	FOS	chr19:56190964-56191301	MCF10A-Er-Src	breast:	n/a	chr19:56191166-56191173 chr19:56191165-56191173
4	FOS	chr19:56190987-56191336	MCF10A-Er-Src	breast:	n/a	chr19:56191166-56191173 chr19:56191165-56191173
5	FOS	chr19:56190926-56191305	HUVEC	blood vessel:	n/a	chr19:56191166-56191173 chr19:56191165-56191173
6	GATA2	chr19:56190979-56191382	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr19:56190865-56191473	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:56190379-56191730	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:56191149-56191585	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:56190712-56191542	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:56191205-56191380	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:56191201-56192589	K562	blood:	n/a	n/a
13	POLR2A	chr19:56191260-56191597	GM12878	blood:	n/a	n/a
14	STAT3	chr19:56191095-56191244	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56189741..56193540-chr19:56204383..56209311,7	K562	blood:
2	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:

Variant related genes	Relation type
EPN1	TF binding region
ENSG00000211571	TF binding region
ENSG00000267183	chromatin interactions
ENSG00000063244	chromatin interactions
ENSG00000203305	chromatin interactions
ENSG00000267018	chromatin interactions
ENSG00000267117	chromatin interactions

Extended variants
information (count: 8 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs564146143	chr19:56191246-56191247	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
2	rs7249837	chr19:56191270-56191271	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs543165870	chr19:56191289-56191290	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
4	rs34960032	chr19:56191319-56191320	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
5	rs111973248	chr19:56191321-56191322	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
6	rs563875475	chr19:56191334-56191335	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
7	rs529470462	chr19:56191338-56191339	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
8	rs549613918	chr19:56191342-56191343	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Breast cancer	20459607	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Alzheimer''s disease	22166940	CNVD
Heart disease	21282601	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Glioblastoma multiforme	21922591	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Breast cancer	21509527	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56187800-56192400	Genic enhancers	Placenta	Placenta
2	chr19:56188000-56192400	Genic enhancers	Fetal Muscle Trunk	muscle
3	chr19:56188200-56192200	Genic enhancers	Esophagus	oesophagus
4	chr19:56188200-56192800	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:56188400-56191600	Genic enhancers	Lung	lung
7	chr19:56188400-56192000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:56188400-56192200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
9	chr19:56188400-56193200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:56188400-56193800	Strong transcription	Brain Cingulate Gyrus	brain
11	chr19:56188400-56194000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:56188400-56195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:56188600-56192800	Genic enhancers	Gastric	stomach
16	chr19:56188600-56193000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr19:56188600-56194000	Strong transcription	A549	lung
18	chr19:56188600-56210000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
21	chr19:56188800-56192800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:56188800-56194000	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr19:56188800-56199800	Weak transcription	HSMMtube	muscle
24	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
25	chr19:56189000-56192200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
26	chr19:56189000-56192600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
27	chr19:56189000-56193400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr19:56189000-56193400	Genic enhancers	Spleen	Spleen
29	chr19:56189000-56199600	Strong transcription	Fetal Stomach	stomach
30	chr19:56189000-56210000	Strong transcription	Fetal Brain Female	brain
31	chr19:56189200-56193200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr19:56189200-56193400	Genic enhancers	Stomach Mucosa	stomach
33	chr19:56189200-56195200	Genic enhancers	Fetal Intestine Small	intestine
34	chr19:56189200-56195400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:56189200-56199400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:56189200-56209400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:56189400-56191600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:56189400-56192000	Genic enhancers	Stomach Smooth Muscle	stomach
40	chr19:56189400-56192200	Weak transcription	Psoas Muscle	Psoas
41	chr19:56189400-56192400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:56189400-56192400	Genic enhancers	Right Ventricle	heart
43	chr19:56189400-56192600	Strong transcription	Aorta	Aorta
44	chr19:56189400-56192600	Genic enhancers	Pancreas	Pancrea
45	chr19:56189400-56193800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:56189400-56193800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:56189400-56194000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr19:56189400-56194000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr19:56189400-56198000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr19:56189400-56199600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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