Variant report

Variant	nsv966517
Chromosome Location	chr4:55593589-55598141
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	ATF2	chr4:55593474-55593941	GM12878	blood:	n/a	n/a
2	BCLAF1	chr4:55593568-55593856	GM12878	blood:	n/a	n/a
3	CHD2	chr4:55593535-55593838	GM12878	blood:	n/a	n/a
4	CTCF	chr4:55593777-55593977	GM12878	blood:	n/a	n/a
5	CTCF	chr4:55593580-55593730	GM06990	blood:	n/a	n/a
6	CTCF	chr4:55593820-55593970	GM06990	blood:	n/a	n/a
7	CUX1	chr4:55593523-55593638	GM12878	blood:	n/a	n/a
8	EBF1	chr4:55597369-55597371	GM12878	blood:	n/a	n/a
9	EBF1	chr4:55593545-55593801	GM12878	blood:	n/a	n/a
10	EBF1	chr4:55594571-55594808	GM12878	blood:	n/a	n/a
11	EP300	chr4:55593399-55593897	GM12878	blood:	n/a	n/a
12	FOS	chr4:55593297-55593589	MCF10A-Er-Src	breast:	n/a	n/a
13	IKZF1	chr4:55593597-55593889	GM12878	blood:	n/a	n/a
14	IRF3	chr4:55593585-55593628	GM12878	blood:	n/a	n/a
15	MAX	chr4:55593312-55593626	GM12878	blood:	n/a	n/a
16	NFIC	chr4:55593384-55593889	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:55595202-55595368	MCF10A-Er-Src	breast:	n/a	n/a
18	RELA	chr4:55593296-55593930	GM12878	blood:	n/a	chr4:55593723-55593732 chr4:55593723-55593732
19	RELA	chr4:55593093-55595399	GM19099	blood:	n/a	chr4:55593723-55593732 chr4:55593723-55593732
20	RELA	chr4:55593192-55594160	GM18951	blood:	n/a	chr4:55593723-55593732 chr4:55593723-55593732
21	RELA	chr4:55593101-55594273	GM19193	blood:	n/a	chr4:55593723-55593732 chr4:55593723-55593732
22	RELA	chr4:55593235-55594157	GM12891	blood:	n/a	chr4:55593723-55593732 chr4:55593723-55593732
23	RELA	chr4:55593235-55594155	GM18505	blood:	n/a	chr4:55593723-55593732 chr4:55593723-55593732
24	SPI1	chr4:55594524-55594929	GM12891	blood:	n/a	n/a
25	SPI1	chr4:55594512-55594832	GM12878	blood:	n/a	n/a
26	SPI1	chr4:55594533-55594826	GM12891	blood:	n/a	n/a
27	SPI1	chr4:55594622-55594785	GM12878	blood:	n/a	n/a
28	STAT3	chr4:55593526-55593697	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT3	chr4:55593476-55593852	GM12878	blood:	n/a	n/a
30	TBL1XR1	chr4:55593482-55593853	GM12878	blood:	n/a	n/a
31	TBP	chr4:55594618-55594951	GM12878	blood:	n/a	n/a
32	ZNF143	chr4:55593669-55593890	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
KIT	TF binding region

Extended variants
information (count: 182 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:182 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs121913235	chr4:55593603-55593604	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs121913511	chr4:55593606-55593607	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs200375589	chr4:55593608-55593609	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs121913685	chr4:55593609-55593610	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs121913517	chr4:55593610-55593611	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs121913521	chr4:55593613-55593614	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs200945282	chr4:55593628-55593629	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs121913513	chr4:55593661-55593662	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs121913680	chr4:55593681-55593682	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs28933371	chr4:55593685-55593686	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs121913515	chr4:55593689-55593690	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs188004213	chr4:55593719-55593720	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs369116250	chr4:55593754-55593755	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs7660233	chr4:55593858-55593859	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs574135703	chr4:55593864-55593865	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs2276949	chr4:55593865-55593866	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs116275848	chr4:55593873-55593874	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs532718067	chr4:55593902-55593903	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs372848340	chr4:55593908-55593909	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs72549291	chr4:55593919-55593920	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs145443303	chr4:55593937-55593938	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs372081193	chr4:55593978-55593979	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs373072016	chr4:55593985-55593986	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs375351432	chr4:55593995-55593996	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs72549292	chr4:55594008-55594009	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs138380197	chr4:55594014-55594015	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs369412402	chr4:55594045-55594046	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs148853099	chr4:55594062-55594063	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs111466688	chr4:55594067-55594068	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs199787524	chr4:55594068-55594069	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs387907217	chr4:55594073-55594074	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs200814065	chr4:55594074-55594075	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs369396078	chr4:55594105-55594106	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs564289653	chr4:55594110-55594111	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs373554876	chr4:55594186-55594187	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs144369407	chr4:55594197-55594198	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs121913512	chr4:55594221-55594222	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs534209826	chr4:55594248-55594249	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs121913523	chr4:55594258-55594259	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs121913679	chr4:55594287-55594288	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs377493174	chr4:55594295-55594296	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs115786802	chr4:55594372-55594373	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs71599651	chr4:55594385-55594386	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs145377313	chr4:55594407-55594408	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs192839740	chr4:55594419-55594420	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs538566622	chr4:55594428-55594429	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs145082774	chr4:55594450-55594451	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs184447387	chr4:55594484-55594485	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs187288350	chr4:55594554-55594555	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs367682148	chr4:55594608-55594609	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
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
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	19435819	CNVD
Multiple myeloma	16616336	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
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
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Ovarian neoplasms	16753589	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	21569311	CNVD
Glioblastoma	17504929	CNVD
Glioblastoma	16823502	CNVD
Melanoma	16908931	CNVD
Glioblastoma	20031968	CNVD
Medulloblastoma	19270706	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Olfactory neuroblastoma	18408657	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Rhabdomyosarcoma	16790082	CNVD
Gastrointestinal stromal cancer	17438095	CNVD
Colorectal cancer	16272173	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	19115005	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	20164920	CNVD
Cancer	22183965	CNVD
Melanoma	18980976	CNVD
Rhabdomyosarcoma	20807811	CNVD

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55557800-55594000	Weak transcription	Aorta	Aorta
2	chr4:55561000-55606600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:55562800-55597400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:55575000-55593600	Weak transcription	NHDF-Ad	bronchial
5	chr4:55576200-55593600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:55576400-55602000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:55576400-55602600	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:55584400-55606200	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:55584800-55596000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:55585200-55608400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:55586200-55595000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:55586600-55604600	Weak transcription	Lung	lung
13	chr4:55587800-55607600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:55588200-55608000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:55588600-55611600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:55589600-55608400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:55589800-55593800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:55589800-55607400	Weak transcription	Left Ventricle	heart
19	chr4:55590000-55603400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:55590000-55608000	Strong transcription	Primary hematopoietic stem cells	blood
21	chr4:55590600-55594000	Weak transcription	Ovary	ovary
22	chr4:55590600-55596000	Weak transcription	Fetal Brain Male	brain
23	chr4:55590600-55602200	Weak transcription	Fetal Brain Female	brain
24	chr4:55591200-55597600	Weak transcription	Fetal Kidney	kidney
25	chr4:55591800-55599200	Weak transcription	Adipose Nuclei	Adipose
26	chr4:55592000-55593600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr4:55592200-55593600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr4:55592600-55609000	Weak transcription	Fetal Stomach	stomach
29	chr4:55592800-55593600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr4:55592800-55593800	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr4:55593000-55594800	Enhancers	Primary B cells from cord blood	blood
32	chr4:55593200-55594000	Flanking Active TSS	GM12878-XiMat	blood
33	chr4:55593200-55594400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr4:55593200-55594400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:55593200-55594400	Enhancers	HUVEC	blood vessel
36	chr4:55593200-55595600	Enhancers	Primary B cells from peripheral blood	blood
37	chr4:55593400-55593600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr4:55593400-55593800	Genic enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:55593400-55593800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:55593400-55595000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:55593400-55595000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr4:55593400-55596200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr4:55593400-55598200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:55593400-55607200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr4:55593600-55593800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
46	chr4:55593600-55594000	Strong transcription	NHDF-Ad	bronchial
47	chr4:55593600-55594400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:55593600-55594400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:55593600-55602600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:55593600-55606800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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