Variant report

Variant	esv3392058
Chromosome Location	chr10:42400406-42402277
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	chr10:42397869..42400416-chr19:27731046..27733513,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BMS1-12	chr10:42400201-42400696	NONHSAT012847

Extended variants
information (count: 583 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:583 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs74212011	chr10:42400408-42400409	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs200364988	chr10:42400410-42400411	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs200680786	chr10:42400411-42400412	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs74221311	chr10:42400412-42400413	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs74192046	chr10:42400415-42400416	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs66528015	chr10:42400416-42400417	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs71251242	chr10:42400417-42400418	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs71288176	chr10:42400419-42400420	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs74185653	chr10:42400420-42400421	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs36154425	chr10:42400421-42400422	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs12257470	chr10:42400422-42400423	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs71297962	chr10:42400423-42400424	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs78222994	chr10:42400424-42400425	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs199906030	chr10:42400425-42400426	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs74210485	chr10:42400427-42400428	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs567347635	chr10:42400429-42400430	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs74203938	chr10:42400431-42400432	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs1584530	chr10:42400432-42400433	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs71233012	chr10:42400434-42400435	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs74198359	chr10:42400439-42400440	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs79345640	chr10:42400440-42400441	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs371914379	chr10:42400442-42400443	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs369491084	chr10:42400448-42400449	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs74210129	chr10:42400452-42400453	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs74202738	chr10:42400453-42400454	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs372516755	chr10:42400455-42400456	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs200256844	chr10:42400456-42400457	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs530020527	chr10:42400457-42400458	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs369174659	chr10:42400459-42400460	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs549902938	chr10:42400461-42400462	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs71243581	chr10:42400470-42400471	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs112550402	chr10:42400471-42400472	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs538710059	chr10:42400472-42400473	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs372593551	chr10:42400473-42400474	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs71275524	chr10:42400475-42400476	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs71225721	chr10:42400476-42400477	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs558733162	chr10:42400478-42400479	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs9702847	chr10:42400485-42400486	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs71224162	chr10:42400486-42400487	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs201049480	chr10:42400487-42400488	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs71247892	chr10:42400488-42400489	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs71263535	chr10:42400490-42400491	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs1839356	chr10:42400491-42400492	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs565708828	chr10:42400492-42400493	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs71305254	chr10:42400493-42400494	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs74188877	chr10:42400494-42400495	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs200000688	chr10:42400495-42400496	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs534946090	chr10:42400497-42400498	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs36160221	chr10:42400504-42400505	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs36191543	chr10:42400506-42400507	ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Pancreatic endocrine tumor	17639061	CNVD
Gastric cancer	17908304	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Melanoma	18172304	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Lung cancer	18438408	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	20724749	CNVD
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Autism	18414403	CNVD
Cockayne syndrome	18421352	CNVD
Glioblastoma	16823260	CNVD
Medulloblastoma	16968546	CNVD
Neuroblastoma	17533364	CNVD
Mental retardation	21062444	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Testicular germ cell tumor	18059402	CNVD
Squamous cell cancer	21044232	CNVD
Glioma	21971842	CNVD
Cancer	21637783	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	20858243	CNVD
Obesity	20622171	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	22241247	CNVD
Intellectual disability	21811512	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Obesity	21956041	CNVD
Lung cancer	21569311	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Renal cell carcinoma	18765545	CNVD
Breast cancer	21785460	CNVD
Ovarian cancer	21781307	CNVD

Chromatin state (count:264 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:42373600-42400800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
2	chr10:42373600-42400800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:42373600-42400800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:42373600-42400800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:42373600-42400800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr10:42373600-42400800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:42373600-42400800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
8	chr10:42373600-42400800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
9	chr10:42373600-42400800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:42373600-42400800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
11	chr10:42373600-42400800	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr10:42373600-42400800	ZNF genes & repeats	Brain Angular Gyrus	brain
13	chr10:42373600-42400800	ZNF genes & repeats	Brain Anterior Caudate	brain
14	chr10:42373600-42400800	ZNF genes & repeats	Brain Hippocampus Middle	brain
15	chr10:42373600-42400800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
16	chr10:42373600-42400800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:42373600-42400800	ZNF genes & repeats	Brain Substantia Nigra	brain
18	chr10:42373600-42400800	ZNF genes & repeats	Colon Smooth Muscle	Colon
19	chr10:42373600-42400800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
20	chr10:42373600-42400800	ZNF genes & repeats	Fetal Heart	heart
21	chr10:42373600-42400800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr10:42373600-42400800	ZNF genes & repeats	Fetal Lung	lung
23	chr10:42373600-42400800	ZNF genes & repeats	Gastric	stomach
24	chr10:42373600-42400800	ZNF genes & repeats	Left Ventricle	heart
25	chr10:42373600-42400800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
26	chr10:42373600-42400800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
27	chr10:42373600-42400800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
28	chr10:42373600-42400800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
29	chr10:42373600-42400800	ZNF genes & repeats	Dnd41	blood
30	chr10:42373600-42400800	ZNF genes & repeats	HMEC	breast
31	chr10:42373600-42400800	ZNF genes & repeats	HSMMtube	muscle
32	chr10:42373600-42400800	ZNF genes & repeats	NH-A	brain
33	chr10:42373600-42401200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
34	chr10:42373600-42402200	ZNF genes & repeats	Colonic Mucosa	Colon
35	chr10:42373600-42402400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
36	chr10:42373600-42402400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
37	chr10:42373600-42402400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:42373600-42402400	ZNF genes & repeats	Fetal Stomach	stomach
39	chr10:42373600-42402600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
40	chr10:42373600-42402600	ZNF genes & repeats	Liver	Liver
41	chr10:42373600-42402600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
42	chr10:42373600-42402600	ZNF genes & repeats	Fetal Brain Male	brain
43	chr10:42373600-42402800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:42373600-42402800	ZNF genes & repeats	HepG2	liver
45	chr10:42373600-42403600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr10:42373600-42405200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr10:42373600-42409400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:42373600-42409400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr10:42373600-42409600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
50	chr10:42373600-42409800	ZNF genes & repeats	Primary T cells from cord blood	blood

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