Variant report

Variant	esv3356414
Chromosome Location	chr19:56103565-56106113
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56096999..56099797-chr19:56105951..56108003,2	MCF-7	breast:
2	chr19:56103233..56104833-chr19:56105149..56107018,2	MCF-7	breast:
3	chr19:56097065..56098659-chr19:56102630..56104410,2	MCF-7	breast:
4	chr19:56103233..56104833-chr19:56105149..56107018,2	MCF-7	breast:
5	chr19:56101839..56104195-chr19:56150974..56153633,2	K562	blood:
6	chr19:56098773..56102057-chr19:56102785..56106000,5	K562	blood:
7	chr19:56098521..56100588-chr19:56100809..56103773,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213015	chromatin interactions
ENSG00000171425	chromatin interactions
ENSG00000173581	chromatin interactions

Extended variants
information (count: 109 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:109 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557880277	chr19:56103575-56103576	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs565494481	chr19:56103579-56103580	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs576480401	chr19:56103586-56103587	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs575774295	chr19:56103591-56103592	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs11469855	chr19:56103614-56103615	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs569823232	chr19:56103615-56103616	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs368340053	chr19:56103631-56103632	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs112608783	chr19:56103644-56103645	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs561607912	chr19:56103673-56103674	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs530112575	chr19:56103732-56103733	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs547018333	chr19:56103741-56103742	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs74937583	chr19:56103742-56103743	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs532654748	chr19:56103756-56103757	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs369823783	chr19:56103767-56103768	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs191295027	chr19:56103783-56103784	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs146737852	chr19:56103789-56103790	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs201003413	chr19:56103828-56103829	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs550454124	chr19:56103831-56103832	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs377755621	chr19:56103864-56103865	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs200475461	chr19:56103882-56103883	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs535803438	chr19:56103915-56103916	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs141118393	chr19:56103978-56103979	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs138734721	chr19:56104077-56104078	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs184489129	chr19:56104078-56104079	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs149341884	chr19:56104079-56104080	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs373766893	chr19:56104084-56104085	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs376358672	chr19:56104107-56104108	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs199729395	chr19:56104118-56104119	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs572821124	chr19:56104134-56104135	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs7247236	chr19:56104136-56104137	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs367627715	chr19:56104137-56104138	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs370245327	chr19:56104140-56104141	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs558403776	chr19:56104144-56104145	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs575783745	chr19:56104147-56104148	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs544865143	chr19:56104151-56104152	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs114339119	chr19:56104152-56104153	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs368962867	chr19:56104155-56104156	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs575221511	chr19:56104172-56104173	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs540598696	chr19:56104187-56104188	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs35748001	chr19:56104191-56104192	Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs35307532	chr19:56104236-56104237	Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs560556456	chr19:56104278-56104279	Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs78940992	chr19:56104327-56104328	Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs140345372	chr19:56104403-56104404	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs112313344	chr19:56104415-56104416	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs546265268	chr19:56104423-56104424	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs562883522	chr19:56104493-56104494	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs10403432	chr19:56104524-56104525	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs10403462	chr19:56104560-56104561	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs567187391	chr19:56104572-56104573	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	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:180 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56097800-56106600	Weak transcription	Aorta	Aorta
2	chr19:56098800-56103600	Weak transcription	Esophagus	oesophagus
3	chr19:56098800-56104800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:56098800-56106200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:56098800-56106200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:56098800-56106200	Weak transcription	Small Intestine	intestine
7	chr19:56098800-56106400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:56098800-56106600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:56098800-56106600	Weak transcription	HSMMtube	muscle
10	chr19:56098800-56109800	Weak transcription	Fetal Heart	heart
11	chr19:56099000-56103600	Weak transcription	Colonic Mucosa	Colon
12	chr19:56099000-56103600	Weak transcription	Gastric	stomach
13	chr19:56099000-56103600	Weak transcription	Lung	lung
14	chr19:56099000-56103600	Weak transcription	NHLF	lung
15	chr19:56099000-56103800	Weak transcription	Right Ventricle	heart
16	chr19:56099000-56105800	Weak transcription	HSMM	muscle
17	chr19:56099000-56106200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:56099000-56106200	Weak transcription	Psoas Muscle	Psoas
19	chr19:56099000-56106200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:56099000-56106800	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:56099000-56106800	Weak transcription	NHDF-Ad	bronchial
22	chr19:56099000-56107000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:56099200-56103600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:56099200-56103600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:56099200-56103600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:56099200-56104800	Weak transcription	NHEK	skin
27	chr19:56099200-56105000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:56099200-56105000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:56099200-56105000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr19:56099200-56105000	Weak transcription	NH-A	brain
31	chr19:56099200-56106200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:56099200-56106200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:56099200-56106200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr19:56099200-56106200	Weak transcription	GM12878-XiMat	blood
35	chr19:56099200-56106200	Weak transcription	Hela-S3	cervix
36	chr19:56099200-56106200	Weak transcription	Osteobl	bone
37	chr19:56099200-56106400	Weak transcription	Fetal Brain Male	brain
38	chr19:56099200-56106400	Weak transcription	Fetal Kidney	kidney
39	chr19:56099200-56106400	Weak transcription	HepG2	liver
40	chr19:56099200-56106400	Weak transcription	HUVEC	blood vessel
41	chr19:56099200-56107000	Weak transcription	HMEC	breast
42	chr19:56099200-56110000	Weak transcription	Right Atrium	heart
43	chr19:56099400-56103600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr19:56099400-56103600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:56099400-56105000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr19:56099400-56106000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr19:56099400-56106400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:56099600-56106200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:56099800-56106200	Weak transcription	Primary B cells from cord blood	blood
50	chr19:56099800-56106200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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