Variant report

Variant	nsv138090
Chromosome Location	chr19:36664841-36667019
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	POLR2A	chr19:36664972-36665103	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:36665385-36665416	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:36666620-36666626	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:36665980-36666171	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr19:36666520-36666624	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:36666357-36666415	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr19:36666016-36666539	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr19:36666270-36666523	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:36666607-36666611	MCF-7	breast:	n/a	n/a
10	POLR2A	chr19:36666642-36666645	MCF-7	breast:	n/a	n/a
11	POLR2A	chr19:36666663-36666673	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:36666124-36666450	A549	lung:	n/a	n/a
13	POLR2A	chr19:36665186-36665382	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:36665281-36665328	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr19:36666377-36666625	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36603757..36607457-chr19:36664359..36667558,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267005	TF binding region
ENSG00000105258	chromatin interactions
ENSG00000105254	chromatin interactions

Extended variants
information (count: 89 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:89 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1559259	chr19:36664898-36664899	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs547008998	chr19:36664932-36664933	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs370656587	chr19:36664948-36664949	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs545799532	chr19:36664955-36664956	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs182845606	chr19:36664969-36664970	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs7247502	chr19:36665007-36665008	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs572819414	chr19:36665086-36665087	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs540436169	chr19:36665087-36665088	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs189244562	chr19:36665102-36665103	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs191796945	chr19:36665124-36665125	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs140528129	chr19:36665129-36665130	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs564712060	chr19:36665134-36665135	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs540300270	chr19:36665139-36665140	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs140595039	chr19:36665207-36665208	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs562435804	chr19:36665221-36665222	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs35927732	chr19:36665304-36665305	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs182884594	chr19:36665317-36665318	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs529968455	chr19:36665397-36665398	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs566648123	chr19:36665411-36665412	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs187481620	chr19:36665437-36665438	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs550089014	chr19:36665450-36665451	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs371419876	chr19:36665453-36665454	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs201967185	chr19:36665461-36665462	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs144347438	chr19:36665482-36665483	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs562772580	chr19:36665518-36665519	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs567808463	chr19:36665520-36665521	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs7249000	chr19:36665527-36665528	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs192958998	chr19:36665529-36665530	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs578243929	chr19:36665554-36665555	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs538833134	chr19:36665564-36665565	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs140808178	chr19:36665576-36665577	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs150141491	chr19:36665600-36665601	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs572902312	chr19:36665675-36665676	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs112194392	chr19:36665684-36665685	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs552351002	chr19:36665686-36665687	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs539903338	chr19:36665741-36665742	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs560541495	chr19:36665755-36665756	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs561820472	chr19:36665757-36665758	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs573797370	chr19:36665775-36665776	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs116277231	chr19:36665781-36665782	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs148907395	chr19:36665788-36665789	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs533030471	chr19:36665793-36665794	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs551378995	chr19:36665873-36665874	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs560248465	chr19:36665948-36665949	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs552671135	chr19:36666037-36666038	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs184279791	chr19:36666048-36666049	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs35747960	chr19:36666096-36666097	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs567733524	chr19:36666132-36666133	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs146926523	chr19:36666133-36666134	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs2112971	chr19:36666167-36666168	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:61)

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
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	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
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Ovarian cancer	21397856	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Myelofibrosis	22110671	CNVD
Liver carcinoma	19366792	CNVD
Ovarian cancer	20844748	CNVD
Non-small cell lung cancer	21829676	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Cancer	21183584	CNVD
Honadal dysgenesis	21048976	CNVD
Neurodevelopmental disorder	22521361	CNVD
Endometrial cancer	23636398	CNVD
Disorders of sex development	21048976	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Gastric cancer	21811585	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Glioma	17123091	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36642200-36673400	Weak transcription	Primary B cells from cord blood	blood
2	chr19:36643000-36673800	Weak transcription	NH-A	brain
3	chr19:36643800-36673200	Weak transcription	Brain Germinal Matrix	brain
4	chr19:36644400-36673000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:36644400-36673200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:36644400-36673400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:36644400-36673400	Weak transcription	Brain Angular Gyrus	brain
8	chr19:36652400-36673400	Weak transcription	Fetal Brain Female	brain
9	chr19:36653000-36673400	Weak transcription	Primary T cells from cord blood	blood
10	chr19:36653200-36673200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:36653200-36673200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr19:36653200-36673400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:36653200-36673400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:36653200-36673400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:36653200-36673400	Weak transcription	HMEC	breast
16	chr19:36653200-36673600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:36653200-36681400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:36653200-36684600	Weak transcription	Aorta	Aorta
19	chr19:36655000-36673600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:36655800-36673400	Weak transcription	Fetal Brain Male	brain
21	chr19:36657800-36673400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:36658000-36673600	Weak transcription	Fetal Stomach	stomach
23	chr19:36660000-36673400	Weak transcription	Lung	lung
24	chr19:36660400-36673400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:36660400-36673400	Weak transcription	HSMMtube	muscle
26	chr19:36660400-36673600	Weak transcription	Pancreas	Pancrea
27	chr19:36660600-36673400	Weak transcription	Thymus	Thymus
28	chr19:36660800-36673200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr19:36660800-36673200	Weak transcription	HSMM	muscle
30	chr19:36660800-36673400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:36660800-36673400	Weak transcription	Brain Substantia Nigra	brain
32	chr19:36660800-36673400	Weak transcription	Esophagus	oesophagus
33	chr19:36660800-36673600	Weak transcription	Right Ventricle	heart
34	chr19:36660800-36673600	Weak transcription	Spleen	Spleen
35	chr19:36661800-36668800	Weak transcription	Psoas Muscle	Psoas
36	chr19:36661800-36673000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:36661800-36673000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:36661800-36673000	Weak transcription	Fetal Intestine Small	intestine
39	chr19:36661800-36673200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:36661800-36673200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:36661800-36673200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr19:36661800-36673200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:36661800-36673200	Weak transcription	Adipose Nuclei	Adipose
44	chr19:36661800-36673200	Weak transcription	Liver	Liver
45	chr19:36661800-36673200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:36661800-36673200	Weak transcription	Brain Hippocampus Middle	brain
47	chr19:36661800-36673200	Weak transcription	Colon Smooth Muscle	Colon
48	chr19:36661800-36673200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:36661800-36673200	Weak transcription	Fetal Intestine Large	intestine
50	chr19:36661800-36673200	Weak transcription	Rectal Mucosa Donor 29	rectum

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