Variant report

Variant	esv3346482
Chromosome Location	chr6:53788493-53791691
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:53791060-53791210	AG04450	lung:	n/a	n/a
2	EP300	chr6:53791203-53792612	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr6:53791422-53791681	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr6:53791399-53791683	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr6:53791452-53791683	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr6:53791391-53791652	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL1	chr6:53791274-53792434	HCT-116	colon:	n/a	n/a
8	JUND	chr6:53791330-53792345	HCT-116	colon:	n/a	n/a
9	JUND	chr6:53791191-53791844	HCT-116	colon:	n/a	n/a
10	MAFK	chr6:53791137-53791276	HepG2	liver:	n/a	n/a
11	MAFK	chr6:53791168-53791175	IMR90	lung:	n/a	n/a
12	NFIC	chr6:53791078-53792454	ECC-1	luminal epithelium:	n/a	chr6:53792271-53792287 chr6:53792270-53792287
13	POLR2A	chr6:53790451-53790467	MCF10A-Er-Src	breast:	n/a	n/a
14	SIN3AK20	chr6:53791648-53792352	MCF-7	breast:	n/a	n/a
15	TCF12	chr6:53791149-53792460	ECC-1	luminal epithelium:	n/a	chr6:53792118-53792125
16	TEAD4	chr6:53791344-53791656	ECC-1	luminal epithelium:	n/a	n/a
17	TEAD4	chr6:53791235-53792424	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:53649451..53651865-chr6:53788090..53790923,2	MCF-7	breast:
2	chr6:53669263..53671782-chr6:53791090..53793404,2	MCF-7	breast:
3	chr6:53658327..53660153-chr6:53789681..53791376,2	MCF-7	breast:
4	chr6:53778649..53781585-chr6:53788522..53790145,2	MCF-7	breast:
5	chr6:53791111..53793110-chr6:53802444..53804078,2	MCF-7	breast:
6	chr6:53656777..53661250-chr6:53790077..53794763,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271218	TF binding region
MLIP	TF binding region
ENSG00000236740	TF binding region
ENSG00000228614	chromatin interactions
ENSG00000137269	chromatin interactions

Extended variants
information (count: 107 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:107 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs549966684	chr6:53788498-53788499	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs77827171	chr6:53788534-53788535	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs62396261	chr6:53788540-53788541	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs148590738	chr6:53788600-53788601	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs555675948	chr6:53788622-53788623	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs531890746	chr6:53788625-53788626	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs560674034	chr6:53788674-53788675	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs534369544	chr6:53788689-53788690	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs557727389	chr6:53788737-53788738	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs373224212	chr6:53788812-53788813	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs113591287	chr6:53788854-53788855	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs373448363	chr6:53788879-53788880	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs9474685	chr6:53788882-53788883	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs182263415	chr6:53788914-53788915	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs71558842	chr6:53788998-53788999	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs370275089	chr6:53789013-53789014	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs71558843	chr6:53789019-53789020	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs74425672	chr6:53789020-53789021	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs542826868	chr6:53789029-53789030	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs542967823	chr6:53789086-53789087	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs7742165	chr6:53789123-53789124	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs116296124	chr6:53789235-53789236	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs372794118	chr6:53789252-53789253	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs562886703	chr6:53789267-53789268	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs533129112	chr6:53789357-53789358	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs151098890	chr6:53789362-53789363	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs80254227	chr6:53789384-53789385	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs535682557	chr6:53789412-53789413	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs115850468	chr6:53789460-53789461	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs140377131	chr6:53789490-53789491	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs535337524	chr6:53789534-53789535	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs186047582	chr6:53789545-53789546	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs558124267	chr6:53789576-53789577	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs189362659	chr6:53789620-53789621	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs78469143	chr6:53789634-53789635	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs114365268	chr6:53789674-53789675	Weak transcription Enhancers Genic enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs573754575	chr6:53789695-53789696	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs71558844	chr6:53789738-53789739	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs542888482	chr6:53789809-53789810	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs9370243	chr6:53789830-53789831	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs71558845	chr6:53789837-53789838	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs375059523	chr6:53789860-53789861	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs181119238	chr6:53789874-53789875	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs71558846	chr6:53789922-53789923	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs59230346	chr6:53789933-53789934	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs398001617	chr6:53789946-53789947	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs113205328	chr6:53789964-53789965	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs572910527	chr6:53790168-53790169	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs553397235	chr6:53790189-53790190	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs143029942	chr6:53790194-53790195	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:172 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
2	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
4	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
5	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
8	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
10	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:53769200-53790400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:53772000-53803000	Weak transcription	Lung	lung
14	chr6:53776000-53790600	Weak transcription	Brain Germinal Matrix	brain
15	chr6:53776600-53789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:53776800-53791000	Weak transcription	HUVEC	blood vessel
17	chr6:53777600-53790600	Strong transcription	Fetal Thymus	thymus
18	chr6:53778000-53791800	Weak transcription	Small Intestine	intestine
19	chr6:53779600-53791400	Weak transcription	Placenta	Placenta
20	chr6:53780200-53790400	Weak transcription	Gastric	stomach
21	chr6:53781000-53789200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:53781000-53791200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:53782400-53789400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:53782400-53790400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:53783000-53791400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:53783200-53789400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:53783400-53789800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:53783600-53790800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:53784000-53790200	Weak transcription	Brain Substantia Nigra	brain
30	chr6:53784400-53790400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:53784600-53789000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:53784600-53791600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr6:53784600-53794200	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:53784800-53794000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:53785600-53791400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr6:53785600-53794400	Weak transcription	Thymus	Thymus
37	chr6:53786000-53791800	Weak transcription	Fetal Stomach	stomach
38	chr6:53786000-53794200	Weak transcription	Left Ventricle	heart
39	chr6:53786200-53789000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:53786200-53791000	Weak transcription	NHEK	skin
41	chr6:53786600-53789000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr6:53786600-53791200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:53786600-53791400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:53786600-53791600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:53786800-53789000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:53786800-53791400	Weak transcription	Fetal Kidney	kidney
47	chr6:53786800-53794400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr6:53787000-53789400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr6:53787000-53791200	Weak transcription	Colonic Mucosa	Colon
50	chr6:53787400-53791200	Weak transcription	HSMM	muscle

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