Variant report

Variant	nsv558696
Chromosome Location	chr12:41092666-41172010
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	ATF2	chr12:41095553-41095922	GM12878	blood:	n/a	n/a
2	ATF2	chr12:41095495-41095972	GM12878	blood:	n/a	n/a
3	ATF3	chr12:41112133-41113026	A549	lung:	n/a	n/a
4	ATF3	chr12:41112137-41112996	A549	lung:	n/a	n/a
5	BACH1	chr12:41112882-41112949	H1-hESC	embryonic stem cell:	n/a	n/a
6	BATF	chr12:41095607-41095850	GM12878	blood:	n/a	n/a
7	BATF	chr12:41095547-41095917	GM12878	blood:	n/a	n/a
8	BCL11A	chr12:41095533-41095952	GM12878	blood:	n/a	n/a
9	BCL3	chr12:41112152-41113088	A549	lung:	n/a	n/a
10	BCL3	chr12:41112128-41113731	A549	lung:	n/a	n/a
11	BHLHE40	chr12:41145933-41146140	HepG2	liver:	n/a	n/a
12	BHLHE40	chr12:41112220-41112589	A549	lung:	n/a	n/a
13	CEBPB	chr12:41164416-41164736	A549	lung:	n/a	chr12:41164561-41164572 chr12:41164561-41164574 chr12:41164562-41164573
14	CEBPB	chr12:41164436-41164698	K562	blood:	n/a	chr12:41164561-41164572 chr12:41164561-41164574 chr12:41164562-41164573
15	CEBPB	chr12:41164468-41164721	HepG2	liver:	n/a	chr12:41164561-41164572 chr12:41164561-41164574 chr12:41164562-41164573
16	CEBPB	chr12:41116651-41116831	HepG2	liver:	n/a	chr12:41116736-41116747 chr12:41116736-41116749 chr12:41116737-41116748
17	CEBPB	chr12:41098590-41098896	A549	lung:	n/a	n/a
18	CEBPB	chr12:41111882-41113025	A549	lung:	n/a	chr12:41112729-41112741
19	CEBPB	chr12:41112226-41113067	A549	lung:	n/a	chr12:41112729-41112741
20	CEBPB	chr12:41136111-41136121	H1-hESC	embryonic stem cell:	n/a	n/a
21	CEBPB	chr12:41135344-41135544	HepG2	liver:	n/a	chr12:41135458-41135471
22	CEBPB	chr12:41113250-41113604	A549	lung:	n/a	n/a
23	CEBPB	chr12:41098585-41098918	Hela-S3	cervix:	n/a	n/a
24	CEBPB	chr12:41164478-41164649	H1-hESC	embryonic stem cell:	n/a	chr12:41164561-41164572 chr12:41164561-41164574 chr12:41164562-41164573
25	CEBPB	chr12:41112135-41113710	A549	lung:	n/a	chr12:41112729-41112741
26	CEBPB	chr12:41164425-41164735	IMR90	lung:	n/a	chr12:41164561-41164572 chr12:41164561-41164574 chr12:41164562-41164573
27	CEBPB	chr12:41098485-41098906	A549	lung:	n/a	n/a
28	CREB1	chr12:41112181-41112729	A549	lung:	n/a	n/a
29	CREB1	chr12:41112121-41112501	A549	lung:	n/a	n/a
30	CTCF	chr12:41156020-41156103	GM13977	blood:	n/a	n/a
31	CTCF	chr12:41139280-41139430	HEK293	kidney:	n/a	n/a
32	CTCF	chr12:41139361-41139464	MCF-7	breast:	n/a	n/a
33	CTCF	chr12:41139300-41139450	RPTEC	kidney:	n/a	n/a
34	CTCF	chr12:41139340-41139490	HRPEpiC	eye:	n/a	n/a
35	CTCF	chr12:41156060-41156210	HEEpiC	esophagus:	n/a	n/a
36	CTCF	chr12:41139260-41139410	HCPEpiC	choroid plexus:	n/a	n/a
37	CTCF	chr12:41156040-41156190	HMEC	breast:	n/a	n/a
38	CTCF	chr12:41139353-41139369	Hela-S3	cervix:	n/a	n/a
39	CTCF	chr12:41155960-41156110	GM12873	blood:	n/a	n/a
40	CTCF	chr12:41139320-41139470	BE2_C	brain:	n/a	n/a
41	CTCF	chr12:41139400-41139550	HMEC	breast:	n/a	n/a
42	CTCF	chr12:41139297-41139519	A549	lung:	n/a	n/a
43	CTCF	chr12:41111500-41111650	A549	lung:	n/a	chr12:41111578-41111587
44	CTCF	chr12:41155980-41156130	GM06990	blood:	n/a	n/a
45	CTCF	chr12:41156000-41156150	MCF-7	breast:	n/a	n/a
46	CTCF	chr12:41139340-41139490	GM12874	blood:	n/a	n/a
47	CTCF	chr12:41139320-41139470	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr12:41139260-41139410	BE2_C	brain:	n/a	n/a
49	CTCF	chr12:41139320-41139470	HEEpiC	esophagus:	n/a	n/a
50	CTCF	chr12:41171401-41171462	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:41151197..41153698-chr12:41160986..41163331,2	K562	blood:
2	chr12:41106289..41108607-chr12:41111961..41113819,2	K562	blood:
3	chr12:41106289..41108607-chr12:41111961..41113819,2	K562	blood:
4	chr12:41162174..41163889-chr12:41167656..41170084,3	K562	blood:
5	chr12:41151197..41153698-chr12:41160986..41163331,2	K562	blood:
6	chr12:41162174..41163889-chr12:41167656..41170084,3	K562	blood:
7	chr12:41154089..41156351-chr12:41156663..41158742,2	K562	blood:
8	chr12:41154089..41156351-chr12:41156663..41158742,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC19-3	chr12:41122613-41123699	NONHSAT027743

Variant related genes	Relation type
ENSG00000257680	TF binding region
CNTN1	TF binding region

Extended variants
information (count: 2813 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:2813 , 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	rs2405293	chr12:41092666-41092667	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs35413758	chr12:41092757-41092758	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs527526614	chr12:41092819-41092820	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs546007501	chr12:41092864-41092865	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs139971485	chr12:41092875-41092876	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs201350253	chr12:41092880-41092881	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs113378954	chr12:41092881-41092882	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs71869169	chr12:41092882-41092883	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs59824101	chr12:41092883-41092884	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs201855188	chr12:41092884-41092885	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs199987674	chr12:41092885-41092886	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs139081845	chr12:41092893-41092894	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs546278739	chr12:41092898-41092899	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs143067535	chr12:41092930-41092931	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs371778898	chr12:41092932-41092933	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs188560995	chr12:41092936-41092937	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs561944596	chr12:41092938-41092939	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs56383533	chr12:41092948-41092949	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs115209140	chr12:41093001-41093002	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs547730092	chr12:41093017-41093018	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs150852194	chr12:41093020-41093021	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs557659222	chr12:41093067-41093068	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs551582021	chr12:41093076-41093077	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs180717687	chr12:41093078-41093079	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs368319577	chr12:41093081-41093082	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs139343863	chr12:41093156-41093157	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs556177570	chr12:41093194-41093195	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs185923064	chr12:41093224-41093225	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs189650799	chr12:41093290-41093291	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs535437801	chr12:41093307-41093308	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs75262068	chr12:41093343-41093344	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs10748138	chr12:41093398-41093399	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs546088999	chr12:41093423-41093424	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs367824161	chr12:41093467-41093468	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs564140712	chr12:41093488-41093489	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs182018288	chr12:41093508-41093509	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs144352127	chr12:41093509-41093510	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs11177886	chr12:41093554-41093555	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
39	rs529311114	chr12:41093556-41093557	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs111410321	chr12:41093560-41093561	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs537901772	chr12:41093561-41093562	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs547370653	chr12:41093579-41093580	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs372099113	chr12:41093598-41093599	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs11177887	chr12:41093632-41093633	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs551618871	chr12:41093741-41093742	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs558317585	chr12:41093787-41093788	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs369435120	chr12:41093833-41093834	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs543754292	chr12:41093931-41093932	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs139617980	chr12:41093932-41093933	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs570157148	chr12:41093934-41093935	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	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
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Ewing''s sarcoma	19144156	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41091400-41093800	Enhancers	HMEC	breast
2	chr12:41092000-41092800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:41092000-41094800	Enhancers	A549	lung
4	chr12:41092400-41092800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:41092600-41093800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:41092600-41093800	Enhancers	NHEK	skin
7	chr12:41092600-41097200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:41092800-41093800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:41092800-41121400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:41093800-41121000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:41094800-41095600	Weak transcription	A549	lung
12	chr12:41095600-41096200	Enhancers	A549	lung
13	chr12:41096200-41097400	Weak transcription	A549	lung
14	chr12:41097200-41097400	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr12:41097400-41097800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:41097400-41099200	Enhancers	A549	lung
17	chr12:41097800-41099000	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr12:41098600-41099200	Enhancers	Brain Angular Gyrus	brain
19	chr12:41099000-41101600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:41099200-41102000	Weak transcription	A549	lung
21	chr12:41101600-41101800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr12:41101800-41102200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:41102000-41102800	Enhancers	A549	lung
24	chr12:41102200-41102800	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr12:41102800-41103800	Weak transcription	A549	lung
26	chr12:41102800-41107800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:41103800-41104000	Enhancers	A549	lung
28	chr12:41104000-41104400	Weak transcription	A549	lung
29	chr12:41104400-41105400	Enhancers	A549	lung
30	chr12:41104600-41105600	Enhancers	GM12878-XiMat	blood
31	chr12:41105200-41105800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:41105400-41107600	Weak transcription	A549	lung
33	chr12:41107600-41110200	Enhancers	A549	lung
34	chr12:41107800-41109600	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr12:41108400-41109000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:41109400-41110000	Enhancers	NHEK	skin
37	chr12:41109600-41110000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr12:41109600-41110200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr12:41110000-41112000	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr12:41110200-41110400	Flanking Active TSS	A549	lung
41	chr12:41110400-41110800	Enhancers	A549	lung
42	chr12:41110800-41112000	Flanking Active TSS	A549	lung
43	chr12:41112000-41113000	Active TSS	A549	lung
44	chr12:41112000-41113200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr12:41113000-41113800	Flanking Active TSS	A549	lung
46	chr12:41113200-41113400	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr12:41113800-41115200	Enhancers	A549	lung
48	chr12:41115200-41117000	Weak transcription	A549	lung
49	chr12:41117000-41118600	Enhancers	A549	lung
50	chr12:41118600-41119400	Weak transcription	A549	lung

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