Variant report

Variant	nsv876806
Chromosome Location	chr3:54256648-54330010
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr3:54256397-54256731	HepG2	liver:	n/a	n/a
2	BACH1	chr3:54270926-54270936	H1-hESC	embryonic stem cell:	n/a	n/a
3	BRCA1	chr3:54317620-54317820	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr3:54308849-54308991	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr3:54277947-54278033	Hela-S3	cervix:	n/a	chr3:54277950-54277961
6	CEBPB	chr3:54296982-54297379	Hela-S3	cervix:	n/a	chr3:54297164-54297173 chr3:54297183-54297196 chr3:54297163-54297174 chr3:54297183-54297194 chr3:54297162-54297173
7	CEBPB	chr3:54307895-54308111	K562	blood:	n/a	chr3:54307981-54307992
8	CEBPB	chr3:54306588-54306886	HepG2	liver:	n/a	n/a
9	CEBPB	chr3:54297007-54297360	K562	blood:	n/a	chr3:54297164-54297173 chr3:54297183-54297196 chr3:54297163-54297174 chr3:54297183-54297194 chr3:54297162-54297173
10	CEBPB	chr3:54296987-54297352	A549	lung:	n/a	chr3:54297164-54297173 chr3:54297183-54297196 chr3:54297163-54297174 chr3:54297183-54297194 chr3:54297162-54297173
11	CEBPB	chr3:54307860-54308147	HepG2	liver:	n/a	chr3:54307981-54307992
12	CEBPB	chr3:54296996-54297350	HepG2	liver:	n/a	chr3:54297164-54297173 chr3:54297183-54297196 chr3:54297163-54297174 chr3:54297183-54297194 chr3:54297162-54297173
13	CEBPB	chr3:54297048-54297318	H1-hESC	embryonic stem cell:	n/a	chr3:54297164-54297173 chr3:54297183-54297196 chr3:54297163-54297174 chr3:54297183-54297194 chr3:54297162-54297173
14	CEBPB	chr3:54277881-54278016	K562	blood:	n/a	chr3:54277950-54277961
15	CEBPB	chr3:54308584-54309121	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr3:54256460-54256825	A549	lung:	n/a	n/a
17	CEBPB	chr3:54327764-54328017	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr3:54296943-54297269	A549	lung:	n/a	chr3:54297164-54297173 chr3:54297183-54297196 chr3:54297163-54297174 chr3:54297183-54297194 chr3:54297162-54297173
19	CEBPB	chr3:54277774-54278107	HepG2	liver:	n/a	chr3:54277950-54277961
20	CEBPB	chr3:54296998-54297349	IMR90	lung:	n/a	chr3:54297164-54297173 chr3:54297183-54297196 chr3:54297163-54297174 chr3:54297183-54297194 chr3:54297162-54297173
21	CEBPB	chr3:54328277-54328401	A549	lung:	n/a	chr3:54328323-54328335
22	CEBPB	chr3:54307821-54308154	Hela-S3	cervix:	n/a	chr3:54307981-54307992
23	CEBPB	chr3:54317498-54317873	Hela-S3	cervix:	n/a	chr3:54317680-54317691
24	CHD2	chr3:54317612-54317766	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr3:54286760-54286910	WERI-Rb-1	eye:	n/a	chr3:54286814-54286822
26	CTCF	chr3:54328272-54328561	GM12878	blood:	n/a	chr3:54328394-54328404
27	CTCF	chr3:54328320-54328478	HepG2	liver:	n/a	chr3:54328394-54328404
28	CTCF	chr3:54328388-54328444	GM19238	blood:	n/a	chr3:54328394-54328404
29	CTCF	chr3:54277900-54278050	HBMEC	blood vessel:	n/a	n/a
30	CTCF	chr3:54277620-54277770	A549	lung:	n/a	n/a
31	CTCF	chr3:54328327-54328454	Lung_OC	lung:	n/a	chr3:54328394-54328404
32	CTCF	chr3:54298958-54299034	GM13977	blood:	n/a	n/a
33	CTCF	chr3:54328300-54328450	SK-N-SH_RA	brain:	n/a	chr3:54328394-54328404
34	CTCF	chr3:54260000-54260150	HPAF	blood vessel:	n/a	n/a
35	CTCF	chr3:54277680-54277830	GM12865	blood:	n/a	n/a
36	CTCF	chr3:54286640-54286790	BE2_C	brain:	n/a	n/a
37	CTCF	chr3:54277860-54278010	HCM	heart:	n/a	n/a
38	CTCF	chr3:54328280-54328430	Caco-2	colon:	n/a	chr3:54328394-54328404
39	CTCF	chr3:54328340-54328490	GM12868	blood:	n/a	chr3:54328394-54328404
40	CTCF	chr3:54328423-54328447	LNCaP	prostate:	n/a	n/a
41	CTCF	chr3:54328280-54328430	GM12867	blood:	n/a	chr3:54328394-54328404
42	CTCF	chr3:54328340-54328490	GM12873	blood:	n/a	chr3:54328394-54328404
43	CTCF	chr3:54328320-54328470	Hela-S3	cervix:	n/a	chr3:54328394-54328404
44	CTCF	chr3:54328352-54328497	MCF-7	breast:	n/a	chr3:54328394-54328404
45	CTCF	chr3:54277600-54277750	BE2_C	brain:	n/a	n/a
46	CTCF	chr3:54277620-54277770	HEEpiC	esophagus:	n/a	n/a
47	CTCF	chr3:54328360-54328510	GM12869	blood:	n/a	chr3:54328394-54328404
48	CTCF	chr3:54277640-54277790	HPF	lung:	n/a	n/a
49	CTCF	chr3:54277640-54277790	HCFaa	heart:	n/a	n/a
50	CTCF	chr3:54277700-54277850	HAc	cerebellar:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:54286387..54287180-chr8:129442741..129443555,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL17RB-2	chr3:54306801-54307195	NONHSAT090013

Variant related genes	Relation type
CACNA2D3	TF binding region

Extended variants
information (count: 2829 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:2829 , 50 per page) page: 1 2 3 4 5 6 7 ... 57

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6805548	chr3:54256648-54256649	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs187399142	chr3:54256652-54256653	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs191878050	chr3:54256730-54256731	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs546767359	chr3:54256736-54256737	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs4450860	chr3:54256778-54256779	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs542670108	chr3:54256834-54256835	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs148324453	chr3:54256837-54256838	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs185141199	chr3:54256840-54256841	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs532180389	chr3:54256864-54256865	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs536918945	chr3:54256918-54256919	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs189205571	chr3:54256994-54256995	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs376729859	chr3:54257019-54257020	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs540452642	chr3:54257055-54257056	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs539461810	chr3:54257102-54257103	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs553101917	chr3:54257112-54257113	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs35100472	chr3:54257113-54257114	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs62252197	chr3:54257154-54257155	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs377177743	chr3:54257181-54257182	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs141151153	chr3:54257182-54257183	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs544537171	chr3:54257202-54257203	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs193061721	chr3:54257256-54257257	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs143474275	chr3:54257274-54257275	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs540258199	chr3:54257284-54257285	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs184574527	chr3:54257336-54257337	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs552266125	chr3:54257349-54257350	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs549087531	chr3:54257388-54257389	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs7617999	chr3:54257411-54257412	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs189038465	chr3:54257419-54257420	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs550592390	chr3:54257426-54257427	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs181310586	chr3:54257458-54257459	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs539043233	chr3:54257552-54257553	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs553040556	chr3:54257553-54257554	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs4927993	chr3:54257594-54257595	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs4928014	chr3:54257651-54257652	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs183984524	chr3:54257670-54257671	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs188661602	chr3:54257678-54257679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs375599094	chr3:54257700-54257701	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs544835718	chr3:54257701-54257702	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs62252198	chr3:54257709-54257710	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs533956285	chr3:54257711-54257712	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs150326079	chr3:54257736-54257737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs28855116	chr3:54257763-54257764	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs529254210	chr3:54257764-54257765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs563606932	chr3:54257803-54257804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs542672358	chr3:54257813-54257814	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs563041548	chr3:54257815-54257816	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs202151858	chr3:54257877-54257878	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs200263309	chr3:54257878-54257879	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs368587393	chr3:54257879-54257880	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs60397787	chr3:54257896-54257897	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Glioblastoma multiforme	21080181	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	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
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Lung cancer	16618734	CNVD
Neuroblastoma	19686582	CNVD
Renal cell carcinoma	18765545	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Breast cancer	21509527	CNVD
Prostate cancer	18632612	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:276 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54249800-54260200	Weak transcription	Right Atrium	heart
2	chr3:54252400-54265400	Weak transcription	Pancreas	Pancrea
3	chr3:54252400-54266200	Weak transcription	Esophagus	oesophagus
4	chr3:54256200-54257400	Enhancers	A549	lung
5	chr3:54256400-54257600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr3:54259800-54260000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:54260000-54260200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr3:54260000-54260200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:54260000-54260200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr3:54260000-54260400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:54260000-54260400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:54260000-54260400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:54260000-54260400	Enhancers	Hela-S3	cervix
14	chr3:54260000-54260600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:54260000-54261000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:54260200-54260800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:54260200-54260800	Enhancers	Right Atrium	heart
18	chr3:54260200-54262000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:54260200-54262600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:54260400-54265000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:54260400-54269400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:54260400-54271200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:54260600-54260800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:54260800-54262600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:54260800-54266400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:54261000-54261200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:54261000-54262600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:54261600-54262600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:54262000-54262200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr3:54262200-54262600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:54262600-54263000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr3:54262600-54263000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:54262600-54263000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:54262600-54263000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr3:54262600-54263200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:54262600-54263200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:54262600-54265200	Enhancers	Fetal Brain Female	brain
38	chr3:54262800-54263200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr3:54263600-54264000	Enhancers	Colon Smooth Muscle	Colon
40	chr3:54264400-54265200	Enhancers	Fetal Brain Male	brain
41	chr3:54265000-54265400	Enhancers	Psoas Muscle	Psoas
42	chr3:54265000-54265400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:54265000-54266400	Enhancers	Fetal Muscle Leg	muscle
44	chr3:54265200-54279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:54265400-54278000	Weak transcription	Psoas Muscle	Psoas
46	chr3:54266000-54267200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr3:54266200-54266400	Enhancers	Esophagus	oesophagus
48	chr3:54266200-54266600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr3:54266400-54267200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:54266600-54266800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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