Variant report

Variant	esv3403452
Chromosome Location	chr13:30466852-30468000
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr13:30467556-30467977	SK-N-SH_RA	brain:	n/a	n/a
2	GATA2	chr13:30467664-30468122	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr13:30467497-30468105	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr13:30467480-30468068	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr13:30467644-30467865	SH-SY5Y	brain:	n/a	n/a
6	POLR2A	chr13:30467592-30467981	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr13:30467918-30467967	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr13:30466241-30466906	H1-neurons	neurons:	n/a	n/a
9	REST	chr13:30465968-30467087	H1-neurons	neurons:	n/a	n/a
10	STAT3	chr13:30466820-30467172	MCF10A-Er-Src	breast:	n/a	n/a
11	TCF12	chr13:30467529-30468202	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr13:30467528-30468189	SK-N-SH	brain:	n/a	n/a
13	USF1	chr13:30467622-30467969	SK-N-SH	brain:	n/a	n/a
14	USF1	chr13:30467561-30467940	SK-N-SH_RA	brain:	n/a	n/a
15	USF1	chr13:30467561-30467851	SK-N-SH_RA	brain:	n/a	n/a
16	USF2	chr13:30467634-30467834	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UBL3-5	chr13:30467193-30467612	l_803_chr13:30467192-30468397_testes
2	lnc-UBL3-5	chr13:30467848-30467932	l_803_chr13:30467192-30468397_testes
3	lnc-UBL3-5	chr13:30467299-30467612	NONHSAT032755

No data

Variant related genes	Relation type
LINC00297	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4512947	chr13:30466869-30466870	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs192321144	chr13:30466929-30466930	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs576890128	chr13:30466935-30466936	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs74042857	chr13:30466936-30466937	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs550078496	chr13:30466983-30466984	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs552938667	chr13:30466989-30466990	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs563132359	chr13:30467014-30467015	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs572365408	chr13:30467040-30467041	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs371164462	chr13:30467189-30467190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs371973558	chr13:30467190-30467191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs57111307	chr13:30467219-30467220	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs58144199	chr13:30467223-30467224	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs55755426	chr13:30467228-30467229	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs184574662	chr13:30467337-30467338	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs9508584	chr13:30467377-30467378	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs375083972	chr13:30467387-30467388	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs530260833	chr13:30467464-30467465	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs151021993	chr13:30467475-30467476	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs68066917	chr13:30467476-30467477	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs58691913	chr13:30467478-30467479	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs200184149	chr13:30467479-30467480	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs560661787	chr13:30467529-30467530	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs57167913	chr13:30467579-30467580	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs9508585	chr13:30467597-30467598	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs114665836	chr13:30467647-30467648	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs376630853	chr13:30467793-30467794	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs532658837	chr13:30467816-30467817	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs558166687	chr13:30467819-30467820	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs566087511	chr13:30467836-30467837	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs528382798	chr13:30467937-30467938	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs560802380	chr13:30467958-30467959	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs142491275	chr13:30467959-30467960	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Cancer	20164920	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
HIV/AIDS	22032296	CNVD
Prostate cancer	16705090	CNVD
High-proliferative meningiomas	17937814	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Burkitt''s lymphoma	18698080	CNVD
Chordoma	21602918	CNVD
Bladder cancer	21949216	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Chronic lymphocytic leukemia	21518781	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Ovarian cancer	20844748	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Colorectal cancer	19359472	CNVD
Intracranial aneurysm	19064780	CNVD
Breast cancer	19287154	CNVD
Acute myeloid leukemia	18379011	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Multiple myeloma	17077331	CNVD
Ependymoma	16718352	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Colorectal cancer	16272173	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	21965145	CNVD
Cancer	21183584	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Squamous cell cancer	20885788	CNVD
Thyroid cancer	19087340	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Malignant glioma	17146433	CNVD
Breast cancer	17899364	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Colorectal cancer	16774939	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17133270	CNVD
Myoepithelioma	18604193	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Myelofibrosis	22110671	CNVD
Non-small cell lung cancer	21829676	CNVD
Retinoblastoma	22278416	CNVD
Peters Plus syndrome	16909395	CNVD
Trisomy	24170809	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Breast cancer	20031965	CNVD
Colorectal cancer	19287155	CNVD
Ovarian cancer	19047089	CNVD
Alveolar rhabdomyosarcoma	16790082	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Prostate cancer	18632612	CNVD
Acute lymphoblastic leukemia	18458336	CNVD

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30452200-30468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:30452200-30468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:30452600-30472200	Weak transcription	Ovary	ovary
4	chr13:30462000-30468200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:30462400-30468200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:30463000-30467600	Weak transcription	Fetal Lung	lung
7	chr13:30463000-30468000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:30463000-30476400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:30463400-30468000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr13:30463600-30468000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:30465200-30467000	Enhancers	Brain Substantia Nigra	brain
12	chr13:30466000-30467000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr13:30466000-30467000	Enhancers	Brain Anterior Caudate	brain
14	chr13:30466000-30467000	Enhancers	Brain Hippocampus Middle	brain
15	chr13:30466200-30467000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:30466200-30467000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr13:30466200-30467000	Enhancers	Brain Cingulate Gyrus	brain
18	chr13:30466200-30467000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr13:30466400-30467000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:30466400-30467000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:30466600-30467000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr13:30466600-30467600	Weak transcription	NHDF-Ad	bronchial
23	chr13:30466600-30468000	Weak transcription	Esophagus	oesophagus
24	chr13:30466600-30468200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr13:30466800-30467800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:30466800-30468000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr13:30466800-30468000	Weak transcription	Pancreas	Pancrea
28	chr13:30466800-30468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr13:30466800-30468400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:30467000-30467400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr13:30467000-30467800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr13:30467000-30467800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr13:30467000-30468200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:30467400-30468400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:30467600-30468200	Enhancers	Fetal Intestine Small	intestine
36	chr13:30467600-30468200	Enhancers	Fetal Lung	lung
37	chr13:30467600-30468600	Enhancers	NHDF-Ad	bronchial
38	chr13:30467800-30468000	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr13:30467800-30468400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr13:30467800-30468600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr13:30468000-30468200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:30468000-30468600	Enhancers	H1 Cell Line	embryonic stem cell
43	chr13:30468000-30468600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr13:30468000-30468600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr13:30468000-30468600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:30468000-30468600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr13:30468000-30468600	Enhancers	Esophagus	oesophagus
48	chr13:30468000-30468600	Enhancers	Gastric	stomach
49	chr13:30468000-30468600	Enhancers	Pancreas	Pancrea
50	chr13:30468000-30468600	Enhancers	Sigmoid Colon	Sigmoid Colon

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