Variant report

Variant	esv3356581
Chromosome Location	chr4:3414632-3414983
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	PAX5	chr4:3414426-3414697	GM12878	blood:	n/a	chr4:3414506-3414524
2	POU2F2	chr4:3414665-3415001	GM12878	blood:	n/a	n/a
3	TCF3	chr4:3414568-3414961	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RGS12	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10027926	chr4:3414654-3414655	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs372026309	chr4:3414698-3414699	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs545374293	chr4:3414717-3414718	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs368742955	chr4:3414722-3414723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs565320306	chr4:3414725-3414726	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs368739762	chr4:3414733-3414734	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs531031880	chr4:3414734-3414735	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs529325065	chr4:3414753-3414754	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs111370783	chr4:3414754-3414755	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs77684719	chr4:3414782-3414783	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs111341987	chr4:3414803-3414804	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs113851046	chr4:3414824-3414825	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs13136701	chr4:3414838-3414839	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs550824181	chr4:3414845-3414846	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs113547436	chr4:3414859-3414860	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs372996302	chr4:3414893-3414894	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs563482454	chr4:3414910-3414911	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs529047370	chr4:3414921-3414922	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs112265114	chr4:3414927-3414928	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs565592809	chr4:3414928-3414929	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs535590527	chr4:3414929-3414930	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs534615269	chr4:3414932-3414933	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs550951253	chr4:3414933-3414934	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs556888340	chr4:3414945-3414946	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs148561354	chr4:3414968-3414969	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs537125692	chr4:3414972-3414973	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	21509527	CNVD
Ependymoma	20639864	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3390000-3417200	Weak transcription	Gastric	stomach
2	chr4:3391800-3424200	Weak transcription	Colonic Mucosa	Colon
3	chr4:3392000-3417200	Weak transcription	Pancreas	Pancrea
4	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
5	chr4:3401600-3416200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:3401800-3416000	Weak transcription	Right Ventricle	heart
7	chr4:3403400-3417200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:3405000-3415000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:3405200-3415800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:3405200-3418800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:3406400-3417200	Weak transcription	HMEC	breast
12	chr4:3406600-3417200	Weak transcription	HSMM	muscle
13	chr4:3406800-3415600	Weak transcription	Lung	lung
14	chr4:3406800-3417400	Weak transcription	Aorta	Aorta
15	chr4:3407200-3417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:3407200-3417200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:3407200-3417800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:3407400-3415400	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:3407400-3417800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:3407600-3415400	Weak transcription	Fetal Heart	heart
21	chr4:3407600-3417200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:3407600-3418000	Weak transcription	Left Ventricle	heart
23	chr4:3407800-3417600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:3408200-3416600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:3408600-3417200	Weak transcription	HSMMtube	muscle
26	chr4:3408800-3436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:3409000-3415000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:3409000-3415200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:3409400-3417200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:3409600-3415400	Weak transcription	Fetal Lung	lung
31	chr4:3410400-3415800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:3411000-3415200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:3411000-3415800	Weak transcription	Fetal Intestine Large	intestine
34	chr4:3411000-3416600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:3411000-3417800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:3411000-3436400	Strong transcription	Fetal Intestine Small	intestine
37	chr4:3411200-3436400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:3411200-3436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:3411400-3425600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:3411600-3415200	Weak transcription	Ovary	ovary
41	chr4:3411800-3420000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:3412000-3417200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:3412200-3415600	Weak transcription	HepG2	liver
44	chr4:3412200-3415800	Weak transcription	Spleen	Spleen
45	chr4:3412400-3416000	Weak transcription	Placenta	Placenta
46	chr4:3412400-3417600	Weak transcription	NHEK	skin
47	chr4:3412600-3415000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:3412600-3415200	Weak transcription	Fetal Brain Male	brain
49	chr4:3412600-3416200	Weak transcription	Liver	Liver
50	chr4:3412600-3417800	Weak transcription	Fetal Brain Female	brain

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