Variant report

Variant	esv3382098
Chromosome Location	chr4:3426579-3429102
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr4:3428395-3428652	GM12878	blood:	n/a	chr4:3428501-3428511 chr4:3428500-3428511 chr4:3428502-3428511 chr4:3428502-3428511 chr4:3428500-3428513
2	EBF1	chr4:3428394-3428594	GM12878	blood:	n/a	chr4:3428501-3428511 chr4:3428500-3428511 chr4:3428502-3428511 chr4:3428502-3428511 chr4:3428500-3428513
3	EBF1	chr4:3428374-3428604	GM12878	blood:	n/a	chr4:3428501-3428511 chr4:3428500-3428511 chr4:3428502-3428511 chr4:3428502-3428511 chr4:3428500-3428513
4	FOXA2	chr4:3426729-3427040	A549	lung:	n/a	n/a
5	JUND	chr4:3428664-3428708	K562	blood:	n/a	chr4:3428685-3428694
6	MYC	chr4:3427610-3427657	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:3427476-3427847	HepG2	liver:	n/a	n/a
8	POLR2A	chr4:3426957-3427065	HepG2	liver:	n/a	n/a
9	SPI1	chr4:3428030-3428355	HL-60	blood:	n/a	n/a
10	UBTF	chr4:3428302-3428414	K562	blood:	n/a	n/a
11	YY1	chr4:3428120-3428250	K562	blood:	n/a	chr4:3428223-3428233 chr4:3428211-3428233

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3426534-3426584	RPTEC	kidney:	n/a
2	chr4:3426534-3426584	K562	blood:	n/a
3	chr4:3426534-3426584	HCM	heart:	n/a
4	chr4:3426534-3426584	AoSMC	blood vessel:	n/a
5	chr4:3426534-3426584	NT2-D1	testis:	n/a
6	chr4:3426534-3426584	BJ	skin:	n/a
7	chr4:3426534-3426584	U87	brain:	n/a
8	chr4:3426534-3426584	GM12892	blood:	n/a
9	chr4:3426534-3426584	HRE	kidney:	n/a
10	chr4:3426534-3426584	CMK	blood:	n/a
11	chr4:3426534-3426584	SKMC	muscle:	n/a
12	chr4:3426534-3426584	PFSK-1	brain:	n/a
13	chr4:3426534-3426584	HNPCEpiC	eye:	n/a
14	chr4:3426534-3426584	PANC-1	pancreas:	n/a
15	chr4:3426534-3426584	HL-60	blood:	n/a
16	chr4:3426534-3426584	AG09319	gingival:	n/a
17	chr4:3426534-3426584	BE2_C	brain:	n/a
18	chr4:3426534-3426584	LNCaP	prostate:	n/a
19	chr4:3426534-3426584	HCT-116	colon:	n/a
20	chr4:3426534-3426584	PrEC	prostate:	n/a
21	chr4:3426534-3426584	AG09309	skin:	n/a
22	chr4:3426534-3426584	MCF-7	breast:	n/a
23	chr4:3426534-3426584	HCPEpiC	choroid plexus:	n/a
24	chr4:3426534-3426584	Jurkat	blood:	n/a
25	chr4:3426534-3426584	AG10803	skin:	n/a
26	chr4:3426534-3426584	SAEC	small airway:	n/a
27	chr4:3426534-3426584	SK-N-SH	brain:	n/a
28	chr4:3426534-3426584	AG04449	skin:	fetal
29	chr4:3426534-3426584	GM12891	blood:	n/a
30	chr4:3426534-3426584	MCF10A-Er-Src	breast:	n/a
31	chr4:3426534-3426584	HUVEC	blood vessel:	n/a
32	chr4:3426534-3426584	HAEpiC	amniotic membrane:	n/a
33	chr4:3426534-3426584	GM12878	blood:	n/a
34	chr4:3426534-3426584	HEK293	kidney:	embryo
35	chr4:3426534-3426584	A549	lung:	n/a
36	chr4:3426534-3426584	HRCEpiC	kidney:	n/a
37	chr4:3426534-3426584	HEEpiC	esophagus:	n/a
38	chr4:3426534-3426584	IMR90	lung:	fetal
39	chr4:3426534-3426584	HMEC	breast:	n/a
40	chr4:3426534-3426584	Caco-2	colon:	n/a
41	chr4:3426534-3426584	HPAEpiC	pulmonary alveolar:	n/a
42	chr4:3426534-3426584	NHBE	bronchial:	n/a
43	chr4:3426534-3426584	Hepatocyte	liver:	n/a
44	chr4:3426534-3426584	GM19239	blood:	n/a
45	chr4:3426534-3426584	ovcar-3	ovarian:	n/a
46	chr4:3426534-3426584	ECC-1	luminal epithelium:	n/a
47	chr4:3426534-3426584	Hela-S3	cervix:	n/a
48	chr4:3426534-3426584	HCF	heart:	n/a
49	chr4:3426534-3426584	HIPEpiC	eye:	n/a
50	chr4:3426534-3426584	ProgFib	skin:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:3428890..3430804-chr4:3441748..3443973,2	MCF-7	breast:
2	chr4:3422937..3425880-chr4:3426569..3429789,3	K562	blood:
3	chr4:3422645..3425998-chr4:3426569..3431321,4	K562	blood:
4	chr4:3418487..3420284-chr4:3426920..3428463,2	K562	blood:

No data

Variant related genes	Relation type
RGS12	TF binding region
RGS12	CpG island
ENSG00000159788	chromatin interactions
ENSG00000109758	chromatin interactions

Extended variants
information (count: 114 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:114 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs562420088	chr4:3426590-3426591	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs527659004	chr4:3426639-3426640	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs547773197	chr4:3426643-3426644	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs73079020	chr4:3426659-3426660	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs533510217	chr4:3426662-3426663	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs552378661	chr4:3426690-3426691	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs115721321	chr4:3426708-3426709	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs538051362	chr4:3426730-3426731	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs548153921	chr4:3426775-3426776	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs568345396	chr4:3426787-3426788	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs187419499	chr4:3426788-3426789	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs78968560	chr4:3426805-3426806	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs560140880	chr4:3426825-3426826	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs572314213	chr4:3426840-3426841	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs192887999	chr4:3426855-3426856	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs185077589	chr4:3426862-3426863	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs114980649	chr4:3426869-3426870	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs16844335	chr4:3426889-3426890	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs146372032	chr4:3426904-3426905	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs187897452	chr4:3426915-3426916	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs192784958	chr4:3426916-3426917	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs555739328	chr4:3426920-3426921	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs375461086	chr4:3426981-3426982	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs367841967	chr4:3426996-3426997	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs541062567	chr4:3427004-3427005	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs539001530	chr4:3427022-3427023	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs62275877	chr4:3427040-3427041	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs557110366	chr4:3427071-3427072	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs16844336	chr4:3427075-3427076	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs3748035	chr4:3427088-3427089	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs200217165	chr4:3427103-3427104	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs543526037	chr4:3427117-3427118	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs564985964	chr4:3427118-3427119	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs114176397	chr4:3427137-3427138	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs371848198	chr4:3427141-3427142	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs35767946	chr4:3427143-3427144	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs568252987	chr4:3427151-3427152	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs527633056	chr4:3427206-3427207	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs371939967	chr4:3427215-3427216	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs547059462	chr4:3427231-3427232	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs374843920	chr4:3427238-3427239	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs375852981	chr4:3427241-3427242	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs370211172	chr4:3427242-3427243	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs148923822	chr4:3427247-3427248	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs547375509	chr4:3427299-3427300	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs183853932	chr4:3427315-3427316	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs202216094	chr4:3427333-3427334	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs535634877	chr4:3427359-3427360	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs555972556	chr4:3427360-3427361	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs530413477	chr4:3427378-3427379	Weak transcription Strong transcription	Chromatin interactive 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
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:176 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
2	chr4:3408800-3436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:3411000-3436400	Strong transcription	Fetal Intestine Small	intestine
4	chr4:3411200-3436400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:3411200-3436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:3413600-3437000	Strong transcription	Esophagus	oesophagus
7	chr4:3415000-3435600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:3415000-3436400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:3415400-3437000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:3415600-3433600	Weak transcription	Fetal Kidney	kidney
11	chr4:3415800-3436400	Strong transcription	Lung	lung
12	chr4:3416400-3436200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:3416400-3436800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:3416600-3428200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:3416600-3435600	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:3416600-3437800	Weak transcription	Stomach Mucosa	stomach
17	chr4:3416800-3432000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:3416800-3436600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:3416800-3438400	Weak transcription	NHDF-Ad	bronchial
20	chr4:3417200-3427200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:3417200-3433400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr4:3417200-3435600	Strong transcription	Fetal Intestine Large	intestine
23	chr4:3417200-3444800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:3417400-3427200	Strong transcription	Spleen	Spleen
25	chr4:3417400-3431000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:3417800-3427400	Strong transcription	Primary T cells from cord blood	blood
27	chr4:3417800-3427400	Strong transcription	Brain Hippocampus Middle	brain
28	chr4:3417800-3432800	Weak transcription	Small Intestine	intestine
29	chr4:3417800-3435200	Strong transcription	Adipose Nuclei	Adipose
30	chr4:3417800-3435200	Strong transcription	Fetal Brain Female	brain
31	chr4:3418000-3426800	Strong transcription	Left Ventricle	heart
32	chr4:3418200-3426800	Weak transcription	HUVEC	blood vessel
33	chr4:3418200-3436600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:3418200-3438000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:3418200-3438000	Weak transcription	A549	lung
36	chr4:3418600-3428200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:3419000-3434600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:3419200-3444600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr4:3419400-3438400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:3419600-3435600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:3419600-3438400	Weak transcription	NH-A	brain
42	chr4:3419800-3426600	Weak transcription	HSMM	muscle
43	chr4:3419800-3435200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:3419800-3438800	Weak transcription	NHLF	lung
45	chr4:3420000-3437000	Strong transcription	Brain Germinal Matrix	brain
46	chr4:3420200-3438400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:3420400-3435200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:3420400-3436000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:3420400-3436600	Weak transcription	Fetal Brain Male	brain
50	chr4:3420400-3438200	Weak transcription	Muscle Satellite Cultured Cells	--

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