Variant report

Variant	esv3503217
Chromosome Location	chr19:56211474-56211956
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56204403..56206705-chr19:56209102..56212375,4	MCF-7	breast:
2	chr19:56110891..56112606-chr19:56211484..56213987,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPN1-4	chr19:56211415-56212585	NONHSAT068074

Variant related genes	Relation type
ENSG00000179943	chromatin interactions
ENSG00000171443	chromatin interactions
ENSG00000267117	chromatin interactions

Extended variants
information (count: 25 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs192998686	chr19:56211500-56211501	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
2	rs553410022	chr19:56211531-56211532	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
3	rs573324788	chr19:56211546-56211547	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
4	rs545537810	chr19:56211552-56211553	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
5	rs557921905	chr19:56211564-56211565	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
6	rs577793052	chr19:56211585-56211586	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
7	rs184027971	chr19:56211589-56211590	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
8	rs201279708	chr19:56211637-56211638	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
9	rs563476809	chr19:56211649-56211650	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
10	rs529161905	chr19:56211652-56211653	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
11	rs551828804	chr19:56211708-56211709	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
12	rs8099895	chr19:56211709-56211710	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs138106847	chr19:56211712-56211713	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
14	rs149534116	chr19:56211738-56211739	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
15	rs375199900	chr19:56211748-56211749	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
16	rs188763782	chr19:56211749-56211750	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
17	rs143907550	chr19:56211755-56211756	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
18	rs531057360	chr19:56211777-56211778	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
19	rs4801265	chr19:56211795-56211796	Weak transcription Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs139814335	chr19:56211828-56211829	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
21	rs141486979	chr19:56211848-56211849	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
22	rs368796961	chr19:56211922-56211923	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
23	rs10421319	chr19:56211931-56211932	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs371883954	chr19:56211943-56211944	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
25	rs549262310	chr19:56211956-56211957	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

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
Lung adenocarcinoma	21935476	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
5	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
6	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:56189400-56212400	Strong transcription	Brain Germinal Matrix	brain
8	chr19:56189600-56213200	Strong transcription	Primary T cells from cord blood	blood
9	chr19:56190000-56212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr19:56190200-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:56191000-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:56191800-56218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:56192000-56214600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr19:56192400-56212400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr19:56192800-56213200	Strong transcription	Adipose Nuclei	Adipose
16	chr19:56193200-56214000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:56193600-56213200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:56193800-56212000	Weak transcription	HSMM	muscle
19	chr19:56195000-56212400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:56195400-56217600	Weak transcription	Right Atrium	heart
21	chr19:56197600-56212600	Strong transcription	Lung	lung
22	chr19:56197800-56212400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr19:56199000-56212400	Strong transcription	Liver	Liver
24	chr19:56199200-56214600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:56199600-56213200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:56199800-56212400	Strong transcription	Aorta	Aorta
27	chr19:56200000-56212400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:56200000-56212600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr19:56200000-56213200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:56200000-56216000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:56200400-56212600	Strong transcription	Esophagus	oesophagus
32	chr19:56200600-56212200	Strong transcription	Gastric	stomach
33	chr19:56200600-56212600	Strong transcription	Fetal Stomach	stomach
34	chr19:56200800-56212600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:56200800-56212600	Strong transcription	Placenta	Placenta
36	chr19:56200800-56212600	Strong transcription	Ovary	ovary
37	chr19:56201000-56213000	Weak transcription	K562	blood
38	chr19:56201400-56212200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr19:56201400-56212400	Strong transcription	Fetal Muscle Leg	muscle
40	chr19:56201400-56212600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr19:56201400-56212800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr19:56202000-56212400	Strong transcription	Colonic Mucosa	Colon
43	chr19:56202000-56212400	Strong transcription	Spleen	Spleen
44	chr19:56202200-56212600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr19:56202400-56213000	Strong transcription	Fetal Intestine Small	intestine
46	chr19:56202600-56217000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:56205800-56215400	Weak transcription	NH-A	brain
48	chr19:56206000-56212400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr19:56206000-56212600	Strong transcription	Fetal Intestine Large	intestine
50	chr19:56206600-56215400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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