Variant report

Variant	nsv980303
Chromosome Location	chr4:120358380-120365634
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	FOXA1	chr4:120358719-120359090	HepG2	liver:	n/a	n/a
2	FOXA1	chr4:120358678-120358975	HepG2	liver:	n/a	n/a
3	MYBL2	chr4:120358526-120359126	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:120362493-120362619	HepG2	liver:	n/a	n/a
5	SP1	chr4:120358676-120359006	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE5A-3	chr4:120361716-120361790	NONHSAT098064
2	lnc-PDE5A-3	chr4:120365524-120365586	NONHSAT098064
3	lnc-PDE5A-3	chr4:120362106-120362207	NONHSAT098064

Variant related genes	Relation type
RNU6-1217P	TF binding region

Extended variants
information (count: 285 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:285 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs541616270	chr4:120358402-120358403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs4092729	chr4:120358556-120358557	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs530384267	chr4:120358560-120358561	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs3872803	chr4:120358565-120358566	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs543472404	chr4:120358573-120358574	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs3872804	chr4:120358591-120358592	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs183283619	chr4:120358594-120358595	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs187814367	chr4:120358702-120358703	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs532477759	chr4:120358803-120358804	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs552292158	chr4:120358831-120358832	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs192894846	chr4:120358863-120358864	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs565835685	chr4:120358886-120358887	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs527513020	chr4:120358891-120358892	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs535632678	chr4:120358947-120358948	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs201979917	chr4:120359061-120359062	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs547557103	chr4:120359119-120359120	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs567467134	chr4:120359164-120359165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs71614421	chr4:120359204-120359205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs554595010	chr4:120359216-120359217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs4001305	chr4:120359236-120359237	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs67265404	chr4:120359270-120359271	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs3956481	chr4:120359275-120359276	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs557390671	chr4:120359309-120359310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs71614422	chr4:120359340-120359341	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs558712224	chr4:120359341-120359342	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs572155161	chr4:120359362-120359363	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs76651228	chr4:120359559-120359560	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs187448556	chr4:120359560-120359561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs575032753	chr4:120359577-120359578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs76525361	chr4:120359608-120359609	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs1825059	chr4:120359618-120359619	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs140870069	chr4:120359619-120359620	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs539749999	chr4:120359626-120359627	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs563816604	chr4:120359627-120359628	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs532415426	chr4:120359632-120359633	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs541703399	chr4:120359635-120359636	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs541084510	chr4:120359639-120359640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs545772518	chr4:120359643-120359644	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs559457335	chr4:120359644-120359645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs550069983	chr4:120359650-120359651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs372923970	chr4:120359660-120359661	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs70944874	chr4:120359662-120359663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs370222454	chr4:120359691-120359692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs567407877	chr4:120359698-120359699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs146370162	chr4:120359715-120359716	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs192625463	chr4:120359735-120359736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs368886526	chr4:120359760-120359761	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs75690486	chr4:120359788-120359789	Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
49	rs76833108	chr4:120359806-120359807	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs532086043	chr4:120359826-120359827	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	21183584	CNVD
primary effusion lymphomas	17116491	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Esophageal cancer	21851588	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Colorectal cancer	16272173	CNVD
Testicular germ cell tumor	18059402	CNVD
Ovarian cancer	22174824	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Myelofibrosis	22110671	CNVD
Neuroblastoma	21899760	CNVD
small cell lung cancer	20016488	CNVD
Renal cell carcinoma	18194544	CNVD
Cancer	20164919	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Amyotrophic lateral sclerosis	20685689	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120326600-120360800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:120327200-120361400	Weak transcription	Fetal Intestine Small	intestine
3	chr4:120328800-120375200	Weak transcription	Ovary	ovary
4	chr4:120330200-120367600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:120330600-120365200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:120330600-120366400	Weak transcription	Fetal Stomach	stomach
7	chr4:120336800-120365400	Weak transcription	Fetal Intestine Large	intestine
8	chr4:120341800-120367800	Weak transcription	Adipose Nuclei	Adipose
9	chr4:120345400-120375200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:120349400-120375400	Weak transcription	Lung	lung
11	chr4:120353200-120375000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:120353200-120375200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:120353200-120375200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:120353400-120375200	Weak transcription	Pancreas	Pancrea
15	chr4:120353800-120366000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr4:120354000-120368000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:120354000-120375000	Weak transcription	Placenta	Placenta
18	chr4:120354400-120375200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:120354600-120375200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:120354800-120375600	Weak transcription	Spleen	Spleen
21	chr4:120355000-120375200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:120355200-120375000	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:120355400-120359800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:120355800-120369200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:120355800-120375000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr4:120356600-120363200	Weak transcription	Liver	Liver
27	chr4:120357800-120361400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:120357800-120375000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:120358200-120368600	Weak transcription	Brain Anterior Caudate	brain
30	chr4:120358400-120369600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:120358400-120374800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:120358600-120375200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:120358800-120375200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:120359000-120375400	Weak transcription	Left Ventricle	heart
35	chr4:120359800-120360000	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr4:120360000-120369400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:120360000-120375200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:120360000-120375400	Weak transcription	Brain Substantia Nigra	brain
39	chr4:120360000-120375400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:120360200-120369600	Weak transcription	Gastric	stomach
41	chr4:120360200-120375400	Weak transcription	Esophagus	oesophagus
42	chr4:120360400-120375200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:120360800-120363400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:120360800-120364800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:120361400-120363400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr4:120361400-120370200	Strong transcription	Fetal Intestine Small	intestine
47	chr4:120361400-120375200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:120361400-120375400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr4:120361800-120368800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:120361800-120375200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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