Variant report

Variant	esv3405138
Chromosome Location	chr4:906477-909325
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:428)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr4:909048-909137	GM12878	blood:	n/a	n/a
2	CHD1	chr4:909053-909198	GM12878	blood:	n/a	n/a
3	EP300	chr4:908961-909199	GM12878	blood:	n/a	chr4:909064-909078
4	GABPA	chr4:907617-907991	HepG2	liver:	n/a	n/a
5	MAZ	chr4:909054-909188	GM12878	blood:	n/a	n/a
6	MEF2A	chr4:908920-909151	GM12878	blood:	n/a	n/a
7	MTA3	chr4:908872-909366	GM12878	blood:	n/a	n/a
8	MYC	chr4:908802-908808	MCF-7	breast:	n/a	n/a
9	PAX5	chr4:908845-909063	GM12892	blood:	n/a	n/a
10	PAX5	chr4:908827-909213	GM12878	blood:	n/a	chr4:909064-909073 chr4:909067-909076
11	POLR2A	chr4:907599-907895	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:907931-908110	ProgFib	skin:	n/a	n/a
13	POLR2A	chr4:908470-908962	HepG2	liver:	n/a	n/a
14	POLR2A	chr4:907602-907997	A549	lung:	n/a	n/a
15	POLR2A	chr4:907590-908031	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:908786-909042	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:907486-909156	GM12878	blood:	n/a	n/a
18	POLR2A	chr4:907469-908576	GM12892	blood:	n/a	n/a
19	POLR2A	chr4:907755-907917	ProgFib	skin:	n/a	n/a
20	POLR2A	chr4:908094-908153	HepG2	liver:	n/a	n/a
21	POLR2A	chr4:908115-908178	ProgFib	skin:	n/a	n/a
22	RCOR1	chr4:909080-909190	GM12878	blood:	n/a	n/a
23	REST	chr4:907731-907990	PANC-1	pancreas:	n/a	n/a
24	RUNX3	chr4:908935-909678	GM12878	blood:	n/a	n/a
25	RUNX3	chr4:908801-909309	GM12878	blood:	n/a	n/a
26	SPI1	chr4:908909-909255	GM12878	blood:	n/a	chr4:909069-909076 chr4:909066-909079 chr4:909064-909073
27	SPI1	chr4:908985-909168	GM12878	blood:	n/a	chr4:909069-909076 chr4:909066-909079 chr4:909064-909073
28	SPI1	chr4:908905-909813	HL-60	blood:	n/a	chr4:909069-909076 chr4:909066-909079 chr4:909064-909073
29	SPI1	chr4:908939-909242	GM12891	blood:	n/a	chr4:909069-909076 chr4:909066-909079 chr4:909064-909073
30	SPI1	chr4:908821-909269	GM12891	blood:	n/a	chr4:909069-909076 chr4:909066-909079 chr4:909064-909073
31	TBL1XR1	chr4:908989-909230	GM12878	blood:	n/a	n/a
32	ZNF143	chr4:909092-909292	GM12878	blood:	n/a	n/a

(count:428 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:907758-907808	PFSK-1	brain:	n/a
2	chr4:907758-907808	PFSK-1	brain:	n/a
3	chr4:906860-906910	HRE	kidney:	n/a
4	chr4:907758-907808	GM12878	blood:	n/a
5	chr4:906491-906541	AoSMC	blood vessel:	n/a
6	chr4:906860-906910	PrEC	prostate:	n/a
7	chr4:908859-908909	HRCEpiC	kidney:	n/a
8	chr4:908952-909002	ovcar-3	ovarian:	n/a
9	chr4:907758-907808	HRCEpiC	kidney:	n/a
10	chr4:906491-906541	AG10803	skin:	n/a
11	chr4:907758-907808	Hela-S3	cervix:	n/a
12	chr4:906860-906910	ProgFib	skin:	n/a
13	chr4:906491-906541	HRPEpiC	eye:	n/a
14	chr4:907758-907808	HMEC	breast:	n/a
15	chr4:906491-906541	HIPEpiC	eye:	n/a
16	chr4:907758-907808	HCPEpiC	choroid plexus:	n/a
17	chr4:908859-908909	NT2-D1	testis:	n/a
18	chr4:906491-906541	NH-A	brain:	n/a
19	chr4:906491-906541	HL-60	blood:	n/a
20	chr4:906860-906910	NT2-D1	testis:	n/a
21	chr4:908414-908464	SK-N-SH	brain:	n/a
22	chr4:906741-906791	PrEC	prostate:	n/a
23	chr4:906860-906910	Hela-S3	cervix:	n/a
24	chr4:906860-906910	HEEpiC	esophagus:	n/a
25	chr4:907758-907808	SK-N-SH_RA	brain:	n/a
26	chr4:908859-908909	BE2_C	brain:	n/a
27	chr4:908952-909002	RPTEC	kidney:	n/a
28	chr4:906491-906541	Hepatocyte	liver:	n/a
29	chr4:907758-907808	ovcar-3	ovarian:	n/a
30	chr4:908952-909002	AG09319	gingival:	n/a
31	chr4:907758-907808	BJ	skin:	n/a
32	chr4:906860-906910	HCM	heart:	n/a
33	chr4:908859-908909	NHDF-neo	bronchial:	n/a
34	chr4:907758-907808	HUVEC	blood vessel:	n/a
35	chr4:908859-908909	U87	brain:	n/a
36	chr4:908414-908464	HRPEpiC	eye:	n/a
37	chr4:908414-908464	IMR90	lung:	fetal
38	chr4:906491-906541	GM12891	blood:	n/a
39	chr4:907758-907808	PANC-1	pancreas:	n/a
40	chr4:906860-906910	K562	blood:	n/a
41	chr4:908414-908464	AoSMC	blood vessel:	n/a
42	chr4:908952-909002	LNCaP	prostate:	n/a
43	chr4:908859-908909	AG10803	skin:	n/a
44	chr4:907758-907808	NHDF-neo	bronchial:	n/a
45	chr4:907758-907808	GM12891	blood:	n/a
46	chr4:906741-906791	ECC-1	luminal epithelium:	n/a
47	chr4:907758-907808	NT2-D1	testis:	n/a
48	chr4:908859-908909	SKMC	muscle:	n/a
49	chr4:907758-907808	IMR90	lung:	fetal
50	chr4:908952-909002	ECC-1	luminal epithelium:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:901248..902931-chr4:905387..907765,2	MCF-7	breast:
2	chr4:907859..910508-chr4:1004931..1006480,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DGKQ-2	chr4:907395-907456	NONHSAT094630
2	lnc-DGKQ-2	chr4:909286-909466	NONHSAT094630

No data

Variant related genes	Relation type
GAK	TF binding region
GAK	CpG island
ENSG00000127418	chromatin interactions

Extended variants
information (count: 154 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:154 , 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	rs373364470	chr4:906493-906494	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs35612127	chr4:906512-906513	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs567572883	chr4:906526-906527	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs147271443	chr4:906562-906563	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs376467652	chr4:906569-906570	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs2279178	chr4:906647-906648	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs190858431	chr4:906661-906662	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs182201135	chr4:906679-906680	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs565250791	chr4:906683-906684	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs539099652	chr4:906711-906712	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs557149296	chr4:906730-906731	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs375036501	chr4:906742-906743	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs569051927	chr4:906761-906762	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs536414352	chr4:906768-906769	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs554908386	chr4:906810-906811	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs374939014	chr4:906860-906861	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs540272523	chr4:906861-906862	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs558572167	chr4:906877-906878	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs143435071	chr4:906892-906893	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs6842808	chr4:906903-906904	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs115368685	chr4:906905-906906	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs186280105	chr4:906915-906916	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs542809281	chr4:906916-906917	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs561284661	chr4:906926-906927	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs73209872	chr4:906938-906939	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs559870436	chr4:906973-906974	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs114223252	chr4:906987-906988	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs146733858	chr4:906998-906999	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs532370525	chr4:907026-907027	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs551065030	chr4:907057-907058	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs74616262	chr4:907060-907061	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs375423977	chr4:907095-907096	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs35559451	chr4:907118-907119	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs569210030	chr4:907147-907148	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs58463827	chr4:907167-907168	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs536500914	chr4:907228-907229	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs368177922	chr4:907246-907247	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs372021545	chr4:907264-907265	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs577019752	chr4:907268-907269	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs566807728	chr4:907295-907296	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs148447075	chr4:907298-907299	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs558545507	chr4:907305-907306	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs368915077	chr4:907354-907355	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs190451415	chr4:907357-907358	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs373290132	chr4:907362-907363	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs370718849	chr4:907376-907377	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs556270068	chr4:907377-907378	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs375451505	chr4:907378-907379	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs574439108	chr4:907430-907431	Weak transcription Enhancers Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs377631768	chr4:907498-907499	Weak transcription Enhancers Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
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
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	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
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	21509527	CNVD
Pancreatic cancer	17952125	CNVD
Type 2 diabetes	21754918	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:336 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:841400-907400	Strong transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:842000-907400	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:842200-907600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:844200-907600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr4:847200-920000	Weak transcription	Right Atrium	heart
6	chr4:857400-909600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:858000-907400	Strong transcription	Fetal Stomach	stomach
8	chr4:861800-907400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:873600-907400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr4:873800-919000	Weak transcription	NHDF-Ad	bronchial
11	chr4:875000-907800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:875200-907400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:881600-907400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:881600-907400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:881600-907400	Strong transcription	Gastric	stomach
16	chr4:881800-907200	Weak transcription	Fetal Kidney	kidney
17	chr4:882400-909200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:883000-907400	Strong transcription	Thymus	Thymus
19	chr4:883200-916400	Weak transcription	K562	blood
20	chr4:884400-907200	Weak transcription	A549	lung
21	chr4:887200-909000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr4:888200-913000	Weak transcription	Psoas Muscle	Psoas
23	chr4:889800-909000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:893200-906600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:893600-918200	Weak transcription	HSMM	muscle
26	chr4:896000-907400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:896600-907400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:897000-924800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:899200-916200	Weak transcription	Osteobl	bone
30	chr4:899400-907400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:899600-906800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:899800-906800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:899800-907400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr4:899800-907400	Strong transcription	Dnd41	blood
35	chr4:900000-907400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:900000-907400	Strong transcription	Fetal Intestine Small	intestine
37	chr4:900000-909400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:900400-906800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:900400-907400	Strong transcription	Fetal Intestine Large	intestine
40	chr4:900600-906800	Strong transcription	Fetal Thymus	thymus
41	chr4:900800-907000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:900800-907400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr4:900800-907600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:900800-908200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:900800-915800	Weak transcription	Fetal Brain Male	brain
46	chr4:901000-906800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:901000-907400	Strong transcription	Spleen	Spleen
48	chr4:901200-906600	Strong transcription	Colon Smooth Muscle	Colon
49	chr4:901200-906600	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr4:901200-907200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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