Variant report

Variant	nsv9748
Chromosome Location	chr19:53599536-53603017
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:53601358..53604101-chr19:53630122..53631842,2	MCF-7	breast:
2	chr19:53598253..53601018-chr19:53604672..53606722,3	MCF-7	breast:
3	chr19:53601090..53603099-chr19:53630653..53632192,2	MCF-7	breast:
4	chr19:53596128..53598162-chr19:53599456..53601173,2	MCF-7	breast:
5	chr19:53586275..53589046-chr19:53598456..53600578,2	K562	blood:
6	chr19:53600011..53602788-chr19:53603096..53607332,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170949	chromatin interactions

Extended variants
information (count: 195 )
Associated
traits (count: 68 )

Variant overlapped rSNPs/rCNVs (count:195 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4597436	chr19:53599590-53599591	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs4411612	chr19:53599618-53599619	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs550202458	chr19:53599643-53599644	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs562444447	chr19:53599681-53599682	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs191729633	chr19:53599682-53599683	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs540857180	chr19:53599683-53599684	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs566097752	chr19:53599710-53599711	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs367594621	chr19:53599727-53599728	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs34973263	chr19:53599731-53599732	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs539905533	chr19:53599738-53599739	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs551941717	chr19:53599747-53599748	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs62115438	chr19:53599748-53599749	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs200917502	chr19:53599770-53599771	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs569847303	chr19:53599785-53599786	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs201841985	chr19:53599806-53599807	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs200163523	chr19:53599831-53599832	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs537299847	chr19:53599858-53599859	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs12981958	chr19:53599877-53599878	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs573839796	chr19:53599882-53599883	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs534617873	chr19:53599883-53599884	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs11669168	chr19:53599902-53599903	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs34434320	chr19:53599973-53599974	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs59038863	chr19:53599974-53599975	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs56823013	chr19:53599998-53599999	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs59592867	chr19:53600003-53600004	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs544681934	chr19:53600006-53600007	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs375081222	chr19:53600008-53600009	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs59972442	chr19:53600015-53600016	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs12983079	chr19:53600035-53600036	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs34125120	chr19:53600038-53600039	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs2013185	chr19:53600039-53600040	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs35536190	chr19:53600074-53600075	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs576549601	chr19:53600088-53600089	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs2013241	chr19:53600191-53600192	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs369306058	chr19:53600224-53600225	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs543955173	chr19:53600332-53600333	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs329721	chr19:53600422-53600423	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs529561497	chr19:53600436-53600437	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs1867050	chr19:53600478-53600479	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs3826699	chr19:53600482-53600483	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs533396033	chr19:53600486-53600487	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs369062098	chr19:53600489-53600490	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs570206755	chr19:53600528-53600529	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs530918833	chr19:53600538-53600539	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs1867051	chr19:53600586-53600587	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs147169476	chr19:53600596-53600597	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs537602798	chr19:53600617-53600618	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs34142384	chr19:53600639-53600640	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs1867053	chr19:53600640-53600641	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	mRNA abundance
50	rs147517854	chr19:53600645-53600646	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:68)

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
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Melanoma	17363583	CNVD
Breast cancer	21785460	CNVD
Adrenocortical carcinoma	18281524	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Breast cancer	20459607	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD

Chromatin state (count:328 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53573600-53604800	Weak transcription	Hela-S3	cervix
2	chr19:53574800-53599600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:53575600-53601000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:53576800-53605200	Weak transcription	Stomach Mucosa	stomach
5	chr19:53584600-53599800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:53585200-53599600	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr19:53585400-53604800	Weak transcription	Psoas Muscle	Psoas
8	chr19:53586000-53599600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:53586400-53599800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr19:53586400-53603400	Strong transcription	Primary T cells from cord blood	blood
11	chr19:53586600-53599600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:53586600-53600000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:53586800-53599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:53588200-53601200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr19:53588400-53603400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr19:53588600-53599800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:53589200-53604800	Weak transcription	Fetal Brain Male	brain
18	chr19:53589600-53604800	Weak transcription	Small Intestine	intestine
19	chr19:53590200-53599600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr19:53590400-53605000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr19:53591200-53599600	Genic enhancers	Fetal Intestine Large	intestine
22	chr19:53592800-53604800	Weak transcription	HUVEC	blood vessel
23	chr19:53593400-53599600	ZNF genes & repeats	A549	lung
24	chr19:53594400-53600600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:53594400-53601000	Weak transcription	Primary B cells from cord blood	blood
26	chr19:53594400-53603400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:53594400-53605200	Weak transcription	Fetal Lung	lung
28	chr19:53594600-53600800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr19:53594600-53604800	Weak transcription	Fetal Kidney	kidney
30	chr19:53594600-53604800	Weak transcription	NHEK	skin
31	chr19:53595000-53600000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:53595000-53600800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:53595000-53600800	Weak transcription	Colon Smooth Muscle	Colon
34	chr19:53595000-53600800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr19:53595000-53601000	Weak transcription	Aorta	Aorta
36	chr19:53595000-53601000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:53595000-53601000	Weak transcription	HMEC	breast
38	chr19:53595200-53600600	Weak transcription	Adipose Nuclei	Adipose
39	chr19:53595200-53600800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr19:53595200-53600800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:53595200-53600800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr19:53595200-53600800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr19:53595200-53600800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:53595200-53600800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:53595200-53600800	Weak transcription	NHDF-Ad	bronchial
46	chr19:53595200-53601000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:53595200-53601000	Weak transcription	Gastric	stomach
48	chr19:53595200-53601000	Weak transcription	NHLF	lung
49	chr19:53595200-53601000	Weak transcription	Osteobl	bone
50	chr19:53595200-53601200	Weak transcription	Brain Angular Gyrus	brain

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