Variant report

Variant	nsv1042296
Chromosome Location	chr12:41372512-41401840
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	CEBPB	chr12:41379965-41380229	A549	lung:	n/a	n/a
2	CEBPB	chr12:41385981-41386344	IMR90	lung:	n/a	chr12:41386153-41386166 chr12:41386153-41386164
3	CEBPB	chr12:41385978-41386324	HepG2	liver:	n/a	chr12:41386153-41386166 chr12:41386153-41386164
4	CEBPB	chr12:41390064-41390278	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr12:41385998-41386317	H1-hESC	embryonic stem cell:	n/a	chr12:41386153-41386166 chr12:41386153-41386164
6	CEBPB	chr12:41385987-41386336	K562	blood:	n/a	chr12:41386153-41386166 chr12:41386153-41386164
7	CEBPB	chr12:41385974-41386340	A549	lung:	n/a	chr12:41386153-41386166 chr12:41386153-41386164
8	CTCF	chr12:41378200-41378350	GM12878	blood:	n/a	n/a
9	CTCF	chr12:41400165-41400221	A549	lung:	n/a	n/a
10	CTCF	chr12:41385495-41385497	GM13976	blood:	n/a	n/a
11	CTCF	chr12:41400080-41400230	HEK293	kidney:	n/a	n/a
12	CTCF	chr12:41385502-41385543	GM13976	blood:	n/a	n/a
13	CTCF	chr12:41400120-41400270	NHEK	skin:	n/a	n/a
14	CTCF	chr12:41400206-41400245	MCF-7	breast:	n/a	n/a
15	CTCF	chr12:41389760-41389910	A549	lung:	n/a	n/a
16	CTCF	chr12:41400155-41400159	A549	lung:	n/a	n/a
17	EP300	chr12:41379480-41380662	ECC-1	luminal epithelium:	n/a	chr12:41380431-41380445
18	EP300	chr12:41379693-41380373	A549	lung:	n/a	n/a
19	EP300	chr12:41392843-41393614	ECC-1	luminal epithelium:	n/a	n/a
20	EP300	chr12:41374239-41374488	SK-N-SH_RA	brain:	n/a	n/a
21	EP300	chr12:41379427-41380512	A549	lung:	n/a	chr12:41380431-41380445
22	ESR1	chr12:41379650-41380215	ECC-1	luminal epithelium:	n/a	n/a
23	ESR1	chr12:41393133-41393380	ECC-1	luminal epithelium:	n/a	n/a
24	FOS	chr12:41387193-41387331	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr12:41387059-41387319	HUVEC	blood vessel:	n/a	chr12:41387169-41387180
26	FOSL2	chr12:41379539-41380439	A549	lung:	n/a	n/a
27	FOXA1	chr12:41379614-41380211	ECC-1	luminal epithelium:	n/a	chr12:41380054-41380069
28	FOXA1	chr12:41379978-41380182	ECC-1	luminal epithelium:	n/a	chr12:41380054-41380069
29	FOXA2	chr12:41379810-41380417	A549	lung:	n/a	n/a
30	FOXM1	chr12:41379516-41380403	ECC-1	luminal epithelium:	n/a	n/a
31	FOXM1	chr12:41392899-41393628	ECC-1	luminal epithelium:	n/a	n/a
32	GATA3	chr12:41379460-41380416	A549	lung:	n/a	n/a
33	GATA3	chr12:41374259-41374876	SK-N-SH	brain:	n/a	n/a
34	GATA3	chr12:41379897-41380460	MCF-7	breast:	n/a	n/a
35	GATA3	chr12:41387591-41387875	MCF-7	breast:	n/a	n/a
36	GATA3	chr12:41387650-41387717	SH-SY5Y	brain:	n/a	n/a
37	JUND	chr12:41386053-41386279	HepG2	liver:	n/a	n/a
38	KAP1	chr12:41398665-41399007	HEK293	kidney:	n/a	n/a
39	MXI1	chr12:41376424-41376486	GM12878	blood:	n/a	n/a
40	MYC	chr12:41384641-41384644	NB4	blood:	n/a	n/a
41	NFIC	chr12:41392959-41393478	ECC-1	luminal epithelium:	n/a	n/a
42	NFIC	chr12:41392833-41393568	ECC-1	luminal epithelium:	n/a	n/a
43	NR2F2	chr12:41379909-41380302	MCF-7	breast:	n/a	n/a
44	NR3C1	chr12:41393124-41393345	ECC-1	luminal epithelium:	n/a	n/a
45	NR3C1	chr12:41393129-41393367	ECC-1	luminal epithelium:	n/a	n/a
46	PBX3	chr12:41374488-41374872	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr12:41376790-41376831	ProgFib	skin:	n/a	n/a
48	POLR2A	chr12:41375128-41375157	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr12:41385066-41385141	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr12:41386943-41386948	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:41384285..41386457-chr12:41393196..41395790,2	MCF-7	breast:
2	chr12:41379403..41382000-chr19:56843629..56845735,2	MCF-7	breast:
3	chr12:41384285..41386457-chr12:41393196..41395790,2	MCF-7	breast:

Variant related genes	Relation type
CNTN1	TF binding region

Extended variants
information (count: 1132 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:1132 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs935102	chr12:41372512-41372513	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs147325724	chr12:41372541-41372542	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs563864342	chr12:41372572-41372573	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs182262177	chr12:41372594-41372595	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs544009280	chr12:41372606-41372607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs548857139	chr12:41372626-41372627	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs529592796	chr12:41372644-41372645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs935103	chr12:41372645-41372646	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs184657526	chr12:41372664-41372665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs148378314	chr12:41372670-41372671	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs551890525	chr12:41372684-41372685	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs935104	chr12:41372690-41372691	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs370602617	chr12:41372721-41372722	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs11179286	chr12:41372738-41372739	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs536422838	chr12:41372746-41372747	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs567375556	chr12:41372826-41372827	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs556329200	chr12:41372848-41372849	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs189442947	chr12:41372916-41372917	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs139818559	chr12:41372935-41372936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs181551307	chr12:41372991-41372992	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs185897292	chr12:41372993-41372994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs191230276	chr12:41372996-41372997	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs552106142	chr12:41373013-41373014	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs571683675	chr12:41373076-41373077	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs545427908	chr12:41373127-41373128	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs71449794	chr12:41373145-41373146	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs534667662	chr12:41373224-41373225	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs141608566	chr12:41373247-41373248	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs181343572	chr12:41373254-41373255	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs567234838	chr12:41373287-41373288	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs575753261	chr12:41373316-41373317	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs543604827	chr12:41373317-41373318	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs562317402	chr12:41373328-41373329	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs150514328	chr12:41373358-41373359	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs370568569	chr12:41373360-41373361	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs139499650	chr12:41373370-41373371	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs143244333	chr12:41373434-41373435	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs553025998	chr12:41373492-41373493	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs570119866	chr12:41373564-41373565	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs531045973	chr12:41373593-41373594	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs185934312	chr12:41373745-41373746	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs568246138	chr12:41373797-41373798	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs535315821	chr12:41373858-41373859	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs146222788	chr12:41373876-41373877	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs565651329	chr12:41373930-41373931	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs539017453	chr12:41373960-41373961	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs565843640	chr12:41373961-41373962	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs557332530	chr12:41373962-41373963	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs190718547	chr12:41373963-41373964	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs182395665	chr12:41374010-41374011	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
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
low-grade B-cell lymphoma tumor	18367492	CNVD
Cancer	20164919	CNVD

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41353200-41373600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:41373000-41374600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:41373600-41374800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:41373600-41375200	Enhancers	NHEK	skin
5	chr12:41374000-41374400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:41374000-41374400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr12:41374000-41374400	Enhancers	Fetal Brain Male	brain
8	chr12:41374000-41374400	Enhancers	HMEC	breast
9	chr12:41374000-41374600	Enhancers	Brain Germinal Matrix	brain
10	chr12:41374200-41374600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:41374400-41374600	Enhancers	Brain Angular Gyrus	brain
12	chr12:41374600-41374800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:41374600-41404800	Weak transcription	Brain Angular Gyrus	brain
14	chr12:41374800-41377400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:41374800-41386200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:41377400-41386200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:41378200-41378400	Enhancers	Pancreas	Pancrea
18	chr12:41379400-41380400	Enhancers	A549	lung
19	chr12:41379600-41379800	Enhancers	Colon Smooth Muscle	Colon
20	chr12:41379800-41381200	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:41381200-41383800	Enhancers	Rectal Smooth Muscle	rectum
22	chr12:41381200-41384600	Enhancers	Colon Smooth Muscle	Colon
23	chr12:41381800-41382200	Enhancers	Fetal Stomach	stomach
24	chr12:41381800-41383800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:41382000-41382400	Enhancers	Stomach Smooth Muscle	stomach
26	chr12:41382400-41382800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:41382800-41383400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr12:41382800-41383800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:41382800-41383800	Enhancers	Stomach Smooth Muscle	stomach
30	chr12:41383400-41386400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:41383800-41388400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr12:41384600-41389400	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:41386000-41387800	Enhancers	NHEK	skin
34	chr12:41386200-41386600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr12:41386200-41387600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:41386200-41387800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:41386400-41386800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr12:41386400-41387000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:41386600-41387000	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr12:41387600-41390600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:41387800-41389400	Weak transcription	NHEK	skin
42	chr12:41387800-41389800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:41388400-41388600	Enhancers	Rectal Smooth Muscle	rectum
44	chr12:41388600-41389200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:41389200-41389400	Enhancers	Rectal Smooth Muscle	rectum
46	chr12:41389400-41389600	Enhancers	NHEK	skin
47	chr12:41389400-41389800	Enhancers	Colon Smooth Muscle	Colon
48	chr12:41389800-41392000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:41390600-41391400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:41391400-41392800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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