Variant report

Variant	esv3693109
Chromosome Location	chr12:9863968-9876091
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	chr12:9871635-9871754	HepG2	liver:	n/a	n/a
2	ATF1	chr12:9874056-9874305	K562	blood:	n/a	n/a
3	ATF2	chr12:9872292-9872835	GM12878	blood:	n/a	n/a
4	ATF2	chr12:9873873-9874828	GM12878	blood:	n/a	n/a
5	ATF2	chr12:9874252-9874755	GM12878	blood:	n/a	n/a
6	ATF2	chr12:9869955-9870569	GM12878	blood:	n/a	n/a
7	ATF2	chr12:9865396-9865941	GM12878	blood:	n/a	n/a
8	BACH1	chr12:9864364-9864528	H1-hESC	embryonic stem cell:	n/a	n/a
9	BATF	chr12:9874330-9874684	GM12878	blood:	n/a	n/a
10	BATF	chr12:9867852-9868142	GM12878	blood:	n/a	n/a
11	BATF	chr12:9872349-9872875	GM12878	blood:	n/a	chr12:9872640-9872651
12	BATF	chr12:9864781-9865123	GM12878	blood:	n/a	n/a
13	BATF	chr12:9865511-9866112	GM12878	blood:	n/a	n/a
14	BATF	chr12:9870113-9870455	GM12878	blood:	n/a	n/a
15	BATF	chr12:9872402-9872831	GM12878	blood:	n/a	chr12:9872640-9872651
16	BATF	chr12:9865513-9866092	GM12878	blood:	n/a	n/a
17	BATF	chr12:9864839-9865102	GM12878	blood:	n/a	n/a
18	BCL11A	chr12:9865480-9866093	GM12878	blood:	n/a	n/a
19	BCL11A	chr12:9874449-9874675	GM12878	blood:	n/a	n/a
20	BCL11A	chr12:9874179-9874537	GM12878	blood:	n/a	n/a
21	BCL3	chr12:9873743-9874484	A549	lung:	n/a	n/a
22	BCLAF1	chr12:9870096-9870600	GM12878	blood:	n/a	n/a
23	BCLAF1	chr12:9873976-9874860	GM12878	blood:	n/a	n/a
24	BCLAF1	chr12:9865281-9865730	GM12878	blood:	n/a	n/a
25	BHLHE40	chr12:9874041-9874751	GM12878	blood:	n/a	n/a
26	BHLHE40	chr12:9865712-9865926	GM12878	blood:	n/a	n/a
27	BHLHE40	chr12:9869868-9870566	GM12878	blood:	n/a	n/a
28	BHLHE40	chr12:9870886-9871381	GM12878	blood:	n/a	n/a
29	BRCA1	chr12:9871191-9871363	GM12878	blood:	n/a	n/a
30	BRCA1	chr12:9873878-9874473	Hela-S3	cervix:	n/a	n/a
31	CEBPB	chr12:9873957-9874450	K562	blood:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
32	CEBPB	chr12:9873968-9874515	ECC-1	luminal epithelium:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
33	CEBPB	chr12:9874029-9874553	A549	lung:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
34	CEBPB	chr12:9874109-9874342	HepG2	liver:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
35	CEBPB	chr12:9873926-9874549	A549	lung:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
36	CEBPB	chr12:9873699-9874707	A549	lung:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
37	CEBPB	chr12:9874044-9874445	IMR90	lung:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
38	CEBPB	chr12:9873965-9874607	K562	blood:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
39	CEBPB	chr12:9874076-9874385	K562	blood:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
40	CEBPB	chr12:9874047-9874425	HepG2	liver:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
41	CEBPB	chr12:9865411-9866221	GM12878	blood:	n/a	n/a
42	CEBPB	chr12:9873981-9874510	HCT-116	colon:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
43	CEBPB	chr12:9873941-9874527	ECC-1	luminal epithelium:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
44	CEBPB	chr12:9873933-9874503	MCF-7	breast:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
45	CEBPB	chr12:9874015-9874531	MCF-7	breast:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
46	CEBPB	chr12:9873906-9874688	Hela-S3	cervix:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
47	CEBPB	chr12:9873996-9874435	H1-hESC	embryonic stem cell:	n/a	chr12:9874238-9874247 chr12:9874236-9874249 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874238-9874247 chr12:9874236-9874247
48	CEBPD	chr12:9874073-9874348	K562	blood:	n/a	chr12:9874238-9874247 chr12:9874236-9874247
49	CHD1	chr12:9865481-9865630	GM12878	blood:	n/a	n/a
50	CHD1	chr12:9876044-9876437	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9792708..9795930-chr12:9875976..9879286,3	K562	blood:
2	chr12:9870894..9872831-chr12:9873111..9875756,2	MCF-7	breast:
3	chr12:9801303..9803979-chr12:9875830..9877610,2	K562	blood:
4	chr12:9798330..9801052-chr12:9860989..9864813,3	K562	blood:

Variant related genes	Relation type
CLECL1	TF binding region
ENSG00000256442	chromatin interactions
ENSG00000233719	chromatin interactions
ENSG00000256594	chromatin interactions
ENSG00000272917	chromatin interactions
ENSG00000184293	chromatin interactions

Extended variants
information (count: 312 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:312 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1861089	chr12:9863968-9863969	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs150553126	chr12:9864015-9864016	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs376343119	chr12:9864053-9864054	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs371774567	chr12:9864093-9864094	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs372247979	chr12:9864109-9864110	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs530643236	chr12:9864121-9864122	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs552070881	chr12:9864122-9864123	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs191603905	chr12:9864148-9864149	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs182191535	chr12:9864219-9864220	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs201231716	chr12:9864240-9864241	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs10743815	chr12:9864241-9864242	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs186725276	chr12:9864244-9864245	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs12297721	chr12:9864279-9864280	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs573753261	chr12:9864280-9864281	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs140839069	chr12:9864302-9864303	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs7485402	chr12:9864392-9864393	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs536273388	chr12:9864394-9864395	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs144671050	chr12:9864397-9864398	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs117016846	chr12:9864472-9864473	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs73059569	chr12:9864517-9864518	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs191527347	chr12:9864587-9864588	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs565513180	chr12:9864607-9864608	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs368070550	chr12:9864805-9864806	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs4763819	chr12:9864820-9864821	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs544744412	chr12:9864867-9864868	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs147468104	chr12:9864892-9864893	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs528963921	chr12:9864894-9864895	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs139870877	chr12:9864922-9864923	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs150069043	chr12:9864957-9864958	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs4763283	chr12:9864975-9864976	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs528454711	chr12:9865023-9865024	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs4763820	chr12:9865121-9865122	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs10772062	chr12:9865157-9865158	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs59725988	chr12:9865164-9865165	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs149209783	chr12:9865181-9865182	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs182427586	chr12:9865208-9865209	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs186697082	chr12:9865285-9865286	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs189546734	chr12:9865348-9865349	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs78450795	chr12:9865397-9865398	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs571482237	chr12:9865429-9865430	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs183242813	chr12:9865468-9865469	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs142417017	chr12:9865507-9865508	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs536859211	chr12:9865731-9865732	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs550714753	chr12:9865747-9865748	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs146833665	chr12:9865763-9865764	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs140917371	chr12:9865827-9865828	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs144661917	chr12:9865889-9865890	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs567451909	chr12:9865923-9865924	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs146678714	chr12:9865971-9865972	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs189244408	chr12:9865999-9866000	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Hepatocellular carcinoma	16750200	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Epilepsy	21858020	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Myelofibrosis	22110671	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
craniofacial dysmorphism	21918468	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Alzheimer''s disease	17160897	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21611746	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Autism	20531469	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9840600-9864600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:9858000-9872200	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:9859000-9870200	Enhancers	Primary B cells from cord blood	blood
4	chr12:9860800-9864400	Weak transcription	A549	lung
5	chr12:9861000-9873200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr12:9861000-9874200	Weak transcription	Fetal Thymus	thymus
7	chr12:9861400-9864400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:9861400-9864600	Weak transcription	Primary T cells from cord blood	blood
9	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:9861800-9868200	Enhancers	GM12878-XiMat	blood
11	chr12:9861800-9874000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:9863000-9864000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:9863000-9864000	Enhancers	Placenta	Placenta
14	chr12:9863000-9864600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr12:9863200-9864800	Enhancers	HSMMtube	muscle
16	chr12:9863400-9864800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:9863400-9864800	Enhancers	Fetal Heart	heart
18	chr12:9863600-9864600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr12:9863800-9864000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:9863800-9864600	Enhancers	HSMM	muscle
21	chr12:9863800-9864800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr12:9864000-9865000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:9864000-9873600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:9864200-9864600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:9864200-9864800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:9864400-9864800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr12:9864400-9864800	Enhancers	A549	lung
28	chr12:9864600-9864800	Enhancers	Primary T cells from cord blood	blood
29	chr12:9864600-9864800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:9864800-9865000	Weak transcription	Primary T cells from cord blood	blood
32	chr12:9865600-9865800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:9868200-9868600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:9868200-9869800	Genic enhancers	GM12878-XiMat	blood
35	chr12:9868400-9872600	Weak transcription	HUVEC	blood vessel
36	chr12:9868600-9869200	Enhancers	K562	blood
37	chr12:9868600-9879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:9869200-9874200	Weak transcription	K562	blood
39	chr12:9869800-9870200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
40	chr12:9870200-9870600	Active TSS	GM12878-XiMat	blood
41	chr12:9870200-9871000	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr12:9870600-9871800	Flanking Active TSS	GM12878-XiMat	blood
43	chr12:9870800-9871400	Weak transcription	A549	lung
44	chr12:9871000-9871400	Enhancers	Fetal Intestine Small	intestine
45	chr12:9871000-9874000	Enhancers	Primary B cells from cord blood	blood
46	chr12:9871400-9872000	Enhancers	HepG2	liver
47	chr12:9871400-9873600	Enhancers	A549	lung
48	chr12:9871600-9871800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr12:9871800-9872200	Enhancers	GM12878-XiMat	blood
50	chr12:9872000-9872400	Enhancers	Fetal Brain Male	brain

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