Variant report

Variant	esv3439679
Chromosome Location	chr3:42555248-42559546
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:9)
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	CTCF	chr3:42557618-42557769	NHEK	skin:	n/a	chr3:42557666-42557679
2	CTCF	chr3:42556800-42556950	HMEC	breast:	n/a	n/a
3	CTCF	chr3:42556820-42556970	NHEK	skin:	n/a	n/a
4	CTCF	chr3:42557660-42557810	SAEC	small airway:	n/a	chr3:42557666-42557679
5	CTCF	chr3:42557660-42557810	HEEpiC	esophagus:	n/a	chr3:42557666-42557679
6	CTCF	chr3:42557580-42557730	HMEC	breast:	n/a	chr3:42557666-42557679
7	CTCF	chr3:42557600-42557750	HEEpiC	esophagus:	n/a	chr3:42557666-42557679
8	CTCF	chr3:42557620-42557770	NHEK	skin:	n/a	chr3:42557666-42557679
9	CTCF	chr3:42557646-42557747	Pancreas_OC	pancreas:	n/a	chr3:42557666-42557679
10	CTCF	chr3:42557580-42557730	SAEC	small airway:	n/a	chr3:42557666-42557679
11	CTCF	chr3:42556880-42557030	NHEK	skin:	n/a	n/a
12	E2F4	chr3:42557324-42557502	MCF10A-Er-Src	breast:	n/a	n/a
13	EGR1	chr3:42556904-42557095	K562	blood:	n/a	chr3:42557004-42557015 chr3:42557004-42557015
14	FOS	chr3:42557098-42557503	MCF10A-Er-Src	breast:	n/a	chr3:42557278-42557286
15	FOS	chr3:42556973-42557569	MCF10A-Er-Src	breast:	n/a	chr3:42557278-42557286
16	FOS	chr3:42557102-42557466	MCF10A-Er-Src	breast:	n/a	chr3:42557278-42557286
17	FOS	chr3:42556929-42557640	MCF10A-Er-Src	breast:	n/a	chr3:42557278-42557286
18	FOXA1	chr3:42558632-42558928	T-47D	breast:	n/a	n/a
19	FOXA1	chr3:42558622-42558962	T-47D	breast:	n/a	n/a
20	JUN	chr3:42558444-42558609	K562	blood:	n/a	n/a
21	MYC	chr3:42557037-42557127	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYC	chr3:42557048-42557503	MCF10A-Er-Src	breast:	n/a	n/a
23	MYC	chr3:42556795-42557502	MCF10A-Er-Src	breast:	n/a	chr3:42556849-42556860
24	POLR2A	chr3:42556305-42556527	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr3:42556794-42557173	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr3:42556568-42556656	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:42557170-42557245	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr3:42557175-42557449	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT3	chr3:42557351-42557374	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr3:42557045-42557472	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT3	chr3:42556861-42557375	MCF10A-Er-Src	breast:	n/a	n/a
32	TCF7L2	chr3:42558165-42558265	Hela-S3	cervix:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42556101..42557803-chr3:42559500..42561568,2	K562	blood:
2	chr3:42555090..42557381-chr3:42567941..42570291,2	MCF-7	breast:
3	chr3:42542637..42545106-chr3:42553030..42555271,2	K562	blood:
4	chr3:42543941..42547920-chr3:42554474..42558044,4	K562	blood:
5	chr3:42559156..42562074-chr3:42562895..42565199,3	K562	blood:
6	chr3:42543964..42546152-chr3:42557414..42559017,2	MCF-7	breast:
7	chr3:42558097..42560730-chr3:42575161..42577308,2	MCF-7	breast:
8	chr3:42556101..42557803-chr3:42559500..42561568,2	K562	blood:
9	chr3:42546908..42549650-chr3:42559175..42561054,2	MCF-7	breast:

(count:9 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SEC22C-1	chr3:42558274-42558328	ENSG00000232354.3
2	lnc-SEC22C-1	chr3:42558274-42558328	ENSG00000232354.3
3	lnc-SEC22C-1	chr3:42555097-42555327	ENSG00000232354.3
4	lnc-SEC22C-1	chr3:42558274-42558328	ENSG00000232354.3
5	lnc-SEC22C-1	chr3:42558274-42558328	NONHSAT089224
6	lnc-SEC22C-1	chr3:42558274-42558328	ENSG00000232354.3
7	lnc-SEC22C-1	chr3:42558274-42558328	ENSG00000232354.3
8	lnc-SEC22C-1	chr3:42558274-42558328	ENSG00000232354.3
9	lnc-SEC22C-1	chr3:42558219-42558328	ENSG00000232354.3

No data

Variant related genes	Relation type
VIPR1	TF binding region
ENSG00000114812	chromatin interactions

Extended variants
information (count: 159 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:159 , 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	rs193233046	chr3:42555251-42555252	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs369859970	chr3:42555252-42555253	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs372732994	chr3:42555270-42555271	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs199557126	chr3:42555275-42555276	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs555031811	chr3:42555292-42555293	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs201674548	chr3:42555316-42555317	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs140984283	chr3:42555323-42555324	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs377191964	chr3:42555351-42555352	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs184543016	chr3:42555429-42555430	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs372134199	chr3:42555430-42555431	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs541629296	chr3:42555434-42555435	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs543643526	chr3:42555446-42555447	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs563444261	chr3:42555451-42555452	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs576623852	chr3:42555519-42555520	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs2278215	chr3:42555524-42555525	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs189427166	chr3:42555542-42555543	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs369736183	chr3:42555590-42555591	Weak transcription Genic enhancers Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs547728812	chr3:42555608-42555609	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs564629317	chr3:42555611-42555612	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs533418783	chr3:42555648-42555649	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs549980323	chr3:42555708-42555709	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs79697603	chr3:42555729-42555730	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs535634132	chr3:42555734-42555735	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs77032910	chr3:42555739-42555740	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs192731240	chr3:42555742-42555743	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs116176828	chr3:42555807-42555808	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs143437175	chr3:42555821-42555822	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs571470806	chr3:42555850-42555851	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs537307028	chr3:42555882-42555883	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs183819205	chr3:42555892-42555893	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs573909097	chr3:42555893-42555894	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs146550402	chr3:42555894-42555895	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs527862537	chr3:42555921-42555922	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs552540028	chr3:42555928-42555929	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs144630703	chr3:42555942-42555943	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs2267534	chr3:42555973-42555974	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs532200860	chr3:42555994-42555995	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs541089423	chr3:42556010-42556011	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs111610459	chr3:42556033-42556034	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs66826422	chr3:42556034-42556035	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs34467764	chr3:42556035-42556036	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs397989339	chr3:42556064-42556065	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs55877577	chr3:42556065-42556066	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs11719334	chr3:42556066-42556067	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs61680265	chr3:42556074-42556075	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs533142348	chr3:42556140-42556141	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs144983834	chr3:42556168-42556169	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs563003015	chr3:42556180-42556181	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs529483709	chr3:42556201-42556202	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs549511657	chr3:42556250-42556251	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:86)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Breast cancer	21509527	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD

Chromatin state (count:166 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42547200-42561800	Genic enhancers	Fetal Intestine Small	intestine
2	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:42549200-42561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:42549400-42555800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:42549800-42557000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:42549800-42560600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:42550000-42556000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:42550000-42560400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:42550200-42558200	Enhancers	Right Ventricle	heart
10	chr3:42550400-42555600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:42550600-42558800	Enhancers	Right Atrium	heart
12	chr3:42550800-42555600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:42551200-42559200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr3:42551400-42558800	Enhancers	Left Ventricle	heart
15	chr3:42551600-42555400	Enhancers	Aorta	Aorta
16	chr3:42552200-42555600	Weak transcription	Fetal Heart	heart
17	chr3:42552200-42556400	Weak transcription	Gastric	stomach
18	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
19	chr3:42552400-42558400	Genic enhancers	Rectal Mucosa Donor 31	rectum
20	chr3:42552400-42570000	Weak transcription	Fetal Stomach	stomach
21	chr3:42553000-42555800	Weak transcription	Esophagus	oesophagus
22	chr3:42553000-42556200	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:42553200-42560800	Weak transcription	Small Intestine	intestine
24	chr3:42553400-42556000	Weak transcription	Spleen	Spleen
25	chr3:42553600-42557000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:42553600-42557000	Weak transcription	Liver	Liver
27	chr3:42553600-42559000	Genic enhancers	Lung	lung
28	chr3:42553600-42566600	Weak transcription	Primary B cells from cord blood	blood
29	chr3:42553800-42555400	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr3:42553800-42555600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:42553800-42556400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:42553800-42560400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:42554000-42557800	Weak transcription	Placenta	Placenta
34	chr3:42554000-42559000	Strong transcription	Primary T cells from cord blood	blood
35	chr3:42554000-42560200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:42554200-42556200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:42554400-42555800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:42554400-42558600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:42554600-42555800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:42554600-42556400	Weak transcription	Colonic Mucosa	Colon
41	chr3:42554600-42556800	Genic enhancers	Rectal Mucosa Donor 29	rectum
42	chr3:42554600-42559000	Enhancers	Stomach Mucosa	stomach
43	chr3:42554800-42559200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr3:42555000-42555600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:42555000-42555800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr3:42555000-42556200	Strong transcription	Fetal Intestine Large	intestine
47	chr3:42555000-42556600	Genic enhancers	Duodenum Mucosa	Duodenum
48	chr3:42555000-42557400	Weak transcription	Adipose Nuclei	Adipose
49	chr3:42555200-42556000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:42555200-42556200	Strong transcription	Sigmoid Colon	Sigmoid Colon

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