Variant report

Variant	esv3387765
Chromosome Location	chr4:3030354-3034952
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:3033640-3033790	HepG2	liver:	n/a	n/a
2	CTCF	chr4:3030558-3030627	GM10248	blood:	n/a	n/a
3	CTCF	chr4:3031803-3032077	K562	blood:	n/a	n/a
4	CTCF	chr4:3031802-3032112	K562	blood:	n/a	n/a
5	CTCF	chr4:3033060-3033210	SK-N-SH_RA	brain:	n/a	n/a
6	CTCF	chr4:3031800-3031950	K562	blood:	n/a	n/a
7	CTCF	chr4:3032980-3033130	GM12874	blood:	n/a	n/a
8	CTCF	chr4:3032880-3033030	WERI-Rb-1	eye:	n/a	n/a
9	CTCF	chr4:3031880-3032030	HepG2	liver:	n/a	n/a
10	CTCF	chr4:3032960-3033110	GM12871	blood:	n/a	n/a
11	CTCF	chr4:3032920-3033070	HepG2	liver:	n/a	n/a
12	CTCF	chr4:3032940-3033090	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr4:3031785-3032039	K562	blood:	n/a	n/a
14	CTCF	chr4:3031878-3032026	K562	blood:	n/a	n/a
15	E2F4	chr4:3033145-3033227	MCF10A-Er-Src	breast:	n/a	n/a
16	JUND	chr4:3034465-3034688	HepG2	liver:	n/a	n/a
17	MAX	chr4:3033006-3033545	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr4:3032930-3033573	ECC-1	luminal epithelium:	n/a	n/a
19	MYC	chr4:3031371-3031425	MCF-7	breast:	n/a	n/a
20	MYC	chr4:3032448-3032631	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYC	chr4:3033093-3033293	MCF10A-Er-Src	breast:	n/a	n/a
22	NFIC	chr4:3032888-3033566	ECC-1	luminal epithelium:	n/a	n/a
23	NFIC	chr4:3032898-3033612	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr4:3033008-3033359	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr4:3033355-3033409	K562	blood:	n/a	n/a
26	POLR2A	chr4:3031270-3031459	MCF-7	breast:	n/a	n/a
27	POLR2A	chr4:3031977-3031980	MCF-7	breast:	n/a	n/a
28	POLR2A	chr4:3031988-3032022	MCF-7	breast:	n/a	n/a
29	RAD21	chr4:3031871-3031983	K562	blood:	n/a	n/a
30	RAD21	chr4:3031879-3032025	K562	blood:	n/a	n/a
31	RCOR1	chr4:3031389-3031411	HepG2	liver:	n/a	n/a
32	STAT3	chr4:3033011-3033211	MCF10A-Er-Src	breast:	n/a	n/a
33	STAT3	chr4:3034663-3034771	MCF10A-Er-Src	breast:	n/a	n/a
34	TCF12	chr4:3032970-3033604	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:3028755..3031130-chr4:3031141..3033637,2	K562	blood:
2	chr4:3027654..3029286-chr4:3034423..3037421,2	K562	blood:
3	chr4:3022979..3027638-chr4:3028157..3033306,5	K562	blood:
4	chr4:2963659..2966241-chr4:3031286..3032925,2	MCF-7	breast:
5	chr4:3018174..3020702-chr4:3033149..3035884,2	MCF-7	breast:

No data

Variant related genes	Relation type
GRK4	TF binding region
ENSG00000125388	chromatin interactions
ENSG00000087269	chromatin interactions

Extended variants
information (count: 179 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:179 , 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	rs189684833	chr4:3030400-3030401	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs575567127	chr4:3030438-3030439	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs181993194	chr4:3030447-3030448	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs373414764	chr4:3030502-3030503	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs35200515	chr4:3030503-3030504	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs560919787	chr4:3030507-3030508	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs397808568	chr4:3030516-3030517	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs113429268	chr4:3030522-3030523	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs555218895	chr4:3030543-3030544	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs540388906	chr4:3030548-3030549	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs139330201	chr4:3030555-3030556	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs532376558	chr4:3030599-3030600	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs573614873	chr4:3030602-3030603	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs552112546	chr4:3030650-3030651	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs562885682	chr4:3030680-3030681	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs531880597	chr4:3030694-3030695	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs548793609	chr4:3030701-3030702	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs568544577	chr4:3030706-3030707	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs534367890	chr4:3030764-3030765	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs543853733	chr4:3030788-3030789	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs546399489	chr4:3030794-3030795	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs12696706	chr4:3030797-3030798	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs149608547	chr4:3030804-3030805	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs115306061	chr4:3030810-3030811	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs532896065	chr4:3030853-3030854	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs201530341	chr4:3030915-3030916	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs144681682	chr4:3030932-3030933	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs375243762	chr4:3030956-3030957	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs369779066	chr4:3030958-3030959	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs545054515	chr4:3030959-3030960	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs147908042	chr4:3030968-3030969	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs200663728	chr4:3030969-3030970	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs368670185	chr4:3030988-3030989	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs554816234	chr4:3031005-3031006	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs368881220	chr4:3031015-3031016	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs55852353	chr4:3031016-3031017	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs540379295	chr4:3031017-3031018	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs144354307	chr4:3031085-3031086	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs151005358	chr4:3031089-3031090	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs267600137	chr4:3031096-3031097	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs373078869	chr4:3031114-3031115	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs377547812	chr4:3031120-3031121	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs140903356	chr4:3031125-3031126	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs144771780	chr4:3031129-3031130	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs186171123	chr4:3031130-3031131	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs148787883	chr4:3031133-3031134	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs113244294	chr4:3031153-3031154	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs374489176	chr4:3031174-3031175	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs143922950	chr4:3031190-3031191	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs549733430	chr4:3031206-3031207	Active TSS ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:61)

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
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
Breast cancer	21785460	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2983600-3032000	Weak transcription	Fetal Brain Female	brain
2	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
3	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
4	chr4:3016200-3033200	Weak transcription	Pancreas	Pancrea
5	chr4:3019200-3039000	Weak transcription	Left Ventricle	heart
6	chr4:3021200-3043000	Weak transcription	Brain Germinal Matrix	brain
7	chr4:3024600-3038800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:3024800-3038800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:3025200-3032800	Weak transcription	Fetal Stomach	stomach
10	chr4:3025200-3035200	Weak transcription	Brain Angular Gyrus	brain
11	chr4:3025200-3038800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:3025200-3039000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:3025200-3039000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:3025200-3039000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:3025200-3043400	Weak transcription	Aorta	Aorta
16	chr4:3025400-3031200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:3025400-3033000	Weak transcription	HSMMtube	muscle
18	chr4:3025400-3039000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr4:3025600-3039000	Weak transcription	Fetal Lung	lung
20	chr4:3025600-3042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:3025600-3042800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:3027800-3031200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:3028000-3038400	Weak transcription	Fetal Intestine Small	intestine
24	chr4:3029600-3033000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:3029600-3039000	Weak transcription	Brain Anterior Caudate	brain
26	chr4:3030000-3032800	Weak transcription	Fetal Muscle Leg	muscle
27	chr4:3031200-3031600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:3031200-3033400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:3032000-3032400	Strong transcription	Fetal Brain Female	brain
30	chr4:3032000-3033600	Enhancers	Spleen	Spleen
31	chr4:3032400-3042400	Weak transcription	Fetal Brain Female	brain
32	chr4:3032600-3032800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:3032800-3033000	Bivalent/Poised TSS	HepG2	liver
34	chr4:3032800-3033200	Bivalent Enhancer	Stomach Mucosa	stomach
35	chr4:3032800-3033400	Enhancers	Fetal Stomach	stomach
36	chr4:3032800-3033800	Enhancers	Gastric	stomach
37	chr4:3032800-3034000	Enhancers	Fetal Muscle Trunk	muscle
38	chr4:3032800-3035400	Enhancers	Fetal Muscle Leg	muscle
39	chr4:3033000-3033200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:3033000-3033600	Enhancers	HSMMtube	muscle
41	chr4:3033000-3034400	Bivalent Enhancer	HepG2	liver
42	chr4:3033000-3037800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:3033200-3033400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:3033200-3033600	Enhancers	Pancreas	Pancrea
45	chr4:3033200-3033600	Enhancers	Stomach Mucosa	stomach
46	chr4:3033400-3033600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:3033400-3033600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:3033400-3033600	Enhancers	Stomach Smooth Muscle	stomach
49	chr4:3033400-3034600	Weak transcription	Fetal Stomach	stomach
50	chr4:3033400-3037800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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