Variant report

Variant	esv3529769
Chromosome Location	chr19:56619530-56619843
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	EGR1	chr19:56619445-56619919	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:56619718-56620213	HL-60	blood:	n/a	n/a
3	POLR2A	chr19:56619670-56620999	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:56619722-56620386	A549	lung:	n/a	n/a
5	POLR2A	chr19:56619342-56619810	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:56619745-56620472	GM12892	blood:	n/a	n/a
7	POLR2A	chr19:56617422-56620971	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:56619153-56619717	K562	blood:	n/a	n/a
9	POLR2A	chr19:56619762-56619928	K562	blood:	n/a	n/a
10	POLR2A	chr19:56619364-56619594	H1-hESC	embryonic stem cell:	n/a	n/a
11	REST	chr19:56619759-56620175	PANC-1	pancreas:	n/a	chr19:56619999-56620019 chr19:56619999-56620019 chr19:56620003-56620016 chr19:56619917-56619937 chr19:56620015-56620028 chr19:56620015-56620028
12	SIN3A	chr19:56619536-56619862	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3AK20	chr19:56619818-56620529	PANC-1	pancreas:	n/a	n/a
14	ZNF143	chr19:56619510-56619870	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56619067..56621819-chr19:56683473..56686134,2	K562	blood:
2	chr19:56618269..56620601-chr19:56650918..56652939,2	MCF-7	breast:
3	chr19:56617972..56620643-chr19:56620884..56623590,3	MCF-7	breast:
4	chr19:56618895..56620681-chr19:56648201..56650740,2	K562	blood:
5	chr19:56617470..56621508-chr19:56630958..56634094,7	MCF-7	breast:

Variant related genes	Relation type
ZNF787	TF binding region
ENSG00000167685	chromatin interactions
ENSG00000142409	chromatin interactions

Extended variants
information (count: 12 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs530858280	chr19:56619572-56619573	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs187943344	chr19:56619576-56619577	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs111835416	chr19:56619636-56619637	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs190861679	chr19:56619651-56619652	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs115708572	chr19:56619652-56619653	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs509897	chr19:56619664-56619665	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs187769738	chr19:56619670-56619671	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs565394633	chr19:56619706-56619707	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs528173134	chr19:56619720-56619721	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs192683259	chr19:56619755-56619756	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs571211444	chr19:56619756-56619757	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs536680764	chr19:56619781-56619782	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

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
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
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD

Chromatin state (count:174 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:56602800-56620000	Weak transcription	NH-A	brain
5	chr19:56603200-56619800	Weak transcription	NHDF-Ad	bronchial
6	chr19:56605200-56619800	Weak transcription	HSMM	muscle
7	chr19:56605200-56620000	Weak transcription	Fetal Kidney	kidney
8	chr19:56609600-56619600	Weak transcription	Fetal Heart	heart
9	chr19:56613200-56620000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:56613600-56619800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr19:56615000-56619600	Weak transcription	Brain Substantia Nigra	brain
12	chr19:56615000-56620200	Weak transcription	Aorta	Aorta
13	chr19:56616000-56619800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr19:56616000-56626600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:56616000-56627000	Enhancers	Liver	Liver
16	chr19:56616000-56627200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr19:56616200-56620800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:56616600-56620400	Enhancers	Brain Hippocampus Middle	brain
19	chr19:56617000-56620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:56617200-56619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:56617200-56619800	Enhancers	Primary hematopoietic stem cells	blood
22	chr19:56617200-56619800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr19:56617200-56619800	Strong transcription	Fetal Intestine Small	intestine
24	chr19:56617200-56619800	Weak transcription	Fetal Lung	lung
25	chr19:56617200-56620000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:56617200-56620000	Weak transcription	Fetal Brain Female	brain
27	chr19:56617200-56620000	Weak transcription	HUVEC	blood vessel
28	chr19:56617200-56620400	Weak transcription	Primary T cells from cord blood	blood
29	chr19:56617200-56622000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr19:56617200-56622800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:56617200-56624400	Weak transcription	Hela-S3	cervix
32	chr19:56617200-56629200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:56617400-56620000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:56617400-56620800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:56617400-56620800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr19:56617400-56621000	Genic enhancers	Lung	lung
37	chr19:56617400-56622400	Weak transcription	Fetal Brain Male	brain
38	chr19:56617400-56623400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:56617600-56619600	Genic enhancers	Fetal Muscle Leg	muscle
40	chr19:56617600-56619800	Weak transcription	Colon Smooth Muscle	Colon
41	chr19:56617600-56620000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:56617800-56619600	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr19:56617800-56619800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:56617800-56619800	Weak transcription	Brain Angular Gyrus	brain
45	chr19:56617800-56620400	Genic enhancers	Pancreas	Pancrea
46	chr19:56618000-56619600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
47	chr19:56618000-56619800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:56618000-56621000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr19:56618200-56620000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:56618200-56620200	Enhancers	Gastric	stomach

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