Variant report

Variant	nsv973065
Chromosome Location	chr12:51500579-51501168
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51473248..51478369-chr12:51498942..51502935,5	MCF-7	breast:
2	chr12:51476039..51478259-chr12:51501121..51502687,2	MCF-7	breast:
3	chr12:51474348..51478730-chr12:51495114..51501288,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LETMD1-1	chr12:51500600-51500927	NONHSAT028239

Variant related genes	Relation type
ENSG00000110925	chromatin interactions

Extended variants
information (count: 16 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540359895	chr12:51500621-51500622	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs77859911	chr12:51500671-51500672	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs79903681	chr12:51500704-51500705	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs140627571	chr12:51500724-51500725	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs562807674	chr12:51500732-51500733	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs531686314	chr12:51500830-51500831	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs548201257	chr12:51500850-51500851	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs561701568	chr12:51500874-51500875	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs12580097	chr12:51500886-51500887	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs555841763	chr12:51500893-51500894	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs111927243	chr12:51500894-51500895	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs547491570	chr12:51501007-51501008	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs566917705	chr12:51501036-51501037	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs371800535	chr12:51501045-51501046	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs375194514	chr12:51501097-51501098	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs35839616	chr12:51501160-51501161	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:70)

Disease	PMID	Source
Seminomas	18059402	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Bladder cancer	21909424	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Intracranial ependymoma	16609018	CNVD
Breast cancer	21858162	CNVD
Urothelial carcinoma	21177765	CNVD
Breast cancer	21509527	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Breast cancer	20409316	CNVD
Hodgkin''s lymphoma	18179710	CNVD

Chromatin state (count:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
4	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:51484000-51502000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
11	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:51487200-51502000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:51487200-51505000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr12:51487200-51508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:51487200-51513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr12:51487200-51513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:51487400-51511000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:51487600-51504800	Strong transcription	Adipose Nuclei	Adipose
28	chr12:51487600-51508200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr12:51487600-51512000	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr12:51487800-51505000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:51487800-51505600	Strong transcription	Liver	Liver
32	chr12:51488000-51507600	Strong transcription	Fetal Intestine Large	intestine
33	chr12:51488400-51526600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:51489200-51509400	Weak transcription	Fetal Heart	heart
35	chr12:51493600-51501200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:51493600-51512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:51494000-51503000	Weak transcription	Brain Angular Gyrus	brain
38	chr12:51494200-51501800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:51494400-51515600	Weak transcription	Stomach Mucosa	stomach
40	chr12:51494600-51500600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:51494600-51502200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr12:51494600-51518200	Weak transcription	Esophagus	oesophagus
43	chr12:51494800-51518400	Weak transcription	Aorta	Aorta
44	chr12:51495000-51504000	Weak transcription	Gastric	stomach
45	chr12:51496200-51500600	Weak transcription	Fetal Brain Male	brain
46	chr12:51496400-51500600	Weak transcription	Lung	lung
47	chr12:51496400-51523400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:51497000-51504600	Strong transcription	Hela-S3	cervix
49	chr12:51497600-51502800	Weak transcription	Brain Germinal Matrix	brain
50	chr12:51498000-51500600	Weak transcription	H9 Cell Line	embryonic stem cell

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