Variant report

Variant	esv3412388
Chromosome Location	chr4:3442253-3442648
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:3442235-3442370	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:3442639-3442781	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3442311-3442361	HMEC	breast:	n/a
2	chr4:3442311-3442361	U87	brain:	n/a
3	chr4:3442311-3442361	K562	blood:	n/a
4	chr4:3442311-3442361	BJ	skin:	n/a
5	chr4:3442311-3442361	LNCaP	prostate:	n/a
6	chr4:3442311-3442361	NT2-D1	testis:	n/a
7	chr4:3442311-3442361	SK-N-SH_RA	brain:	n/a
8	chr4:3442311-3442361	MCF10A-Er-Src	breast:	n/a
9	chr4:3442311-3442361	AG04449	skin:	fetal
10	chr4:3442311-3442361	HEEpiC	esophagus:	n/a
11	chr4:3442311-3442361	Hepatocyte	liver:	n/a
12	chr4:3442311-3442361	NHDF-neo	bronchial:	n/a
13	chr4:3442311-3442361	ovcar-3	ovarian:	n/a
14	chr4:3442311-3442361	BE2_C	brain:	n/a
15	chr4:3442311-3442361	ECC-1	luminal epithelium:	n/a
16	chr4:3442311-3442361	SK-N-SH	brain:	n/a
17	chr4:3442311-3442361	HRE	kidney:	n/a
18	chr4:3442311-3442361	HRPEpiC	eye:	n/a
19	chr4:3442311-3442361	SKMC	muscle:	n/a
20	chr4:3442311-3442361	GM12878	blood:	n/a
21	chr4:3442311-3442361	H1-hESC	embryonic stem cell:	embryo
22	chr4:3442311-3442361	HCPEpiC	choroid plexus:	n/a
23	chr4:3442311-3442361	Jurkat	blood:	n/a
24	chr4:3442311-3442361	CMK	blood:	n/a
25	chr4:3442311-3442361	AG09319	gingival:	n/a
26	chr4:3442311-3442361	GM19239	blood:	n/a
27	chr4:3442311-3442361	AG04450	lung:	fetal
28	chr4:3442311-3442361	NB4	blood:	n/a
29	chr4:3442311-3442361	HCT-116	colon:	n/a
30	chr4:3442311-3442361	SAEC	small airway:	n/a
31	chr4:3442311-3442361	HIPEpiC	eye:	n/a
32	chr4:3442311-3442361	PFSK-1	brain:	n/a
33	chr4:3442311-3442361	PANC-1	pancreas:	n/a
34	chr4:3442311-3442361	HAEpiC	amniotic membrane:	n/a
35	chr4:3442311-3442361	HCF	heart:	n/a
36	chr4:3442311-3442361	HL-60	blood:	n/a
37	chr4:3442311-3442361	GM12891	blood:	n/a
38	chr4:3442311-3442361	AG09309	skin:	n/a
39	chr4:3442311-3442361	Caco-2	colon:	n/a
40	chr4:3442311-3442361	HCM	heart:	n/a
41	chr4:3442311-3442361	T-47D	breast:	n/a
42	chr4:3442311-3442361	AG10803	skin:	n/a
43	chr4:3442311-3442361	HRCEpiC	kidney:	n/a
44	chr4:3442311-3442361	A549	lung:	n/a
45	chr4:3442311-3442361	PrEC	prostate:	n/a
46	chr4:3442311-3442361	GM12892	blood:	n/a
47	chr4:3442311-3442361	SK-N-MC	brain:	n/a
48	chr4:3442311-3442361	Hela-S3	cervix:	n/a
49	chr4:3442311-3442361	MCF-7	breast:	n/a
50	chr4:3442311-3442361	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type
1	chr4:3297878..3299647-chr4:3439847..3442316,2	MCF-7	breast:
2	chr4:3416652..3419915-chr4:3441173..3444245,3	MCF-7	breast:
3	chr12:52607035..52609334-chr4:3440706..3442862,2	MCF-7	breast:
4	chr4:3428890..3430804-chr4:3441748..3443973,2	MCF-7	breast:

No data

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

Extended variants
information (count: 18 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs73193400	chr4:3442259-3442260	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs550624631	chr4:3442263-3442264	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs567453888	chr4:3442328-3442329	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs191697206	chr4:3442398-3442399	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs529054957	chr4:3442405-3442406	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs549205027	chr4:3442408-3442409	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs565824489	chr4:3442410-3442411	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs56379800	chr4:3442414-3442415	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs192080705	chr4:3442429-3442430	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs546903183	chr4:3442448-3442449	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs555174274	chr4:3442501-3442502	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs558108923	chr4:3442529-3442530	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs142667333	chr4:3442540-3442541	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs116772679	chr4:3442550-3442551	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs76758203	chr4:3442572-3442573	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs184882913	chr4:3442590-3442591	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs73193402	chr4:3442630-3442631	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs115513037	chr4:3442638-3442639	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:60)

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
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3417200-3444800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:3419200-3444600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr4:3427000-3443200	Weak transcription	Brain Substantia Nigra	brain
4	chr4:3430800-3445200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr4:3431600-3442600	Weak transcription	Colonic Mucosa	Colon
6	chr4:3431800-3444600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:3433000-3445200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:3433200-3444800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:3433600-3444600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:3434200-3442600	Weak transcription	Liver	Liver
11	chr4:3436400-3443000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:3436400-3444400	Weak transcription	Primary T cells from cord blood	blood
13	chr4:3436400-3444400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:3436400-3445200	Weak transcription	Fetal Intestine Small	intestine
15	chr4:3436600-3449000	Weak transcription	Fetal Brain Female	brain
16	chr4:3436800-3443000	Enhancers	Fetal Muscle Leg	muscle
17	chr4:3436800-3445400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:3437000-3442600	Enhancers	Fetal Muscle Trunk	muscle
19	chr4:3437000-3450000	Weak transcription	Brain Germinal Matrix	brain
20	chr4:3437200-3451200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:3437800-3443000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:3438000-3448000	Weak transcription	Right Ventricle	heart
23	chr4:3438600-3444800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:3438800-3445400	Weak transcription	Gastric	stomach
25	chr4:3439000-3445400	Weak transcription	Pancreas	Pancrea
26	chr4:3439200-3445400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:3439400-3442600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr4:3439400-3442600	Weak transcription	NH-A	brain
29	chr4:3439400-3442800	Weak transcription	Osteobl	bone
30	chr4:3439600-3442600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:3440000-3442800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:3440400-3442600	Weak transcription	Esophagus	oesophagus
33	chr4:3440400-3445200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:3440600-3442600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:3441000-3443200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:3441400-3443200	Enhancers	Fetal Lung	lung
37	chr4:3441400-3443800	Enhancers	A549	lung
38	chr4:3441600-3442800	Enhancers	HepG2	liver
39	chr4:3441600-3443200	Enhancers	NHEK	skin
40	chr4:3441600-3443400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:3441800-3442600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr4:3441800-3442800	Enhancers	HMEC	breast
43	chr4:3441800-3443000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:3441800-3443000	Weak transcription	Spleen	Spleen
45	chr4:3442000-3442400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:3442400-3445600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:3442600-3442800	Enhancers	Adipose Nuclei	Adipose
48	chr4:3442600-3443000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:3442600-3443000	Enhancers	NH-A	brain
50	chr4:3442600-3443200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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