Variant report

Variant	nsv524187
Chromosome Location	chr1:241586687-241586834
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	GATA3	chr1:241586689-241587095	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr1:241586821-241586946	ProgFib	skin:	n/a	n/a
3	TCF12	chr1:241586614-241587207	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000225554	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1891129	chr1:241586687-241586688	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs34553496	chr1:241586707-241586708	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs572248766	chr1:241586752-241586753	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs575709248	chr1:241586784-241586785	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs74498101	chr1:241586814-241586815	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs114782125	chr1:241586827-241586828	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs1544190	chr1:241586834-241586835	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Hepatocellular carcinoma	16750200	CNVD
Arrhythmogenic right ventricular cardiomyopathy	17576883	CNVD
Multiple myeloma	16616336	CNVD
Developmental delay	21147756	CNVD
Ovarian cancer	21720365	CNVD
Schizophrenia	17989066	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241574200-241587000	Weak transcription	Gastric	stomach
2	chr1:241584000-241587000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:241585400-241586800	Enhancers	NHLF	lung
4	chr1:241586000-241586800	Active TSS	Brain Anterior Caudate	brain
5	chr1:241586000-241587000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:241586200-241586800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:241586400-241586800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr1:241586600-241586800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:241586600-241586800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:241586600-241586800	Enhancers	Brain Angular Gyrus	brain
11	chr1:241586600-241586800	Enhancers	Brain Substantia Nigra	brain
12	chr1:241586600-241586800	Flanking Active TSS	NHDF-Ad	bronchial
13	chr1:241586600-241586800	Flanking Active TSS	Osteobl	bone
14	chr1:241586600-241587000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr1:241586600-241587000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr1:241586600-241587000	Active TSS	Fetal Brain Male	brain
17	chr1:241586600-241587400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:241586600-241588200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:241586600-241588200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:241586600-241588200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:241586600-241588200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr1:241586800-241587000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
23	chr1:241586800-241587000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:241586800-241587000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
25	chr1:241586800-241587000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr1:241586800-241587000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
27	chr1:241586800-241587000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:241586800-241587000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
29	chr1:241586800-241587000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
30	chr1:241586800-241587000	Active TSS	Brain Hippocampus Middle	brain
31	chr1:241586800-241587000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
32	chr1:241586800-241587000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
33	chr1:241586800-241587000	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr1:241586800-241587000	Bivalent Enhancer	HepG2	liver
35	chr1:241586800-241587000	Active TSS	HMEC	breast
36	chr1:241586800-241587200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
37	chr1:241586800-241587200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:241586800-241587200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:241586800-241587200	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr1:241586800-241587200	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr1:241586800-241587200	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr1:241586800-241587200	Bivalent Enhancer	Fetal Heart	heart
43	chr1:241586800-241587600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:241586800-241587600	Bivalent Enhancer	Liver	Liver
45	chr1:241586800-241587600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:241586800-241587600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
47	chr1:241586800-241587600	Active TSS	HUVEC	blood vessel
48	chr1:241586800-241587600	Active TSS	NH-A	brain
49	chr1:241586800-241587600	Active TSS	NHDF-Ad	bronchial
50	chr1:241586800-241587800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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