Variant report

Variant	nsv1009138
Chromosome Location	chr2:53129701-53167075
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	chr2:53161835-53161893	HepG2	liver:	n/a	n/a
2	ATF2	chr2:53161550-53162230	GM12878	blood:	n/a	n/a
3	ATF2	chr2:53161624-53162186	GM12878	blood:	n/a	n/a
4	ATF3	chr2:53161366-53162095	HCT-116	colon:	n/a	n/a
5	BATF	chr2:53161569-53162046	GM12878	blood:	n/a	chr2:53161802-53161813 chr2:53161799-53161809 chr2:53161784-53161795
6	BATF	chr2:53166348-53166822	GM12878	blood:	n/a	n/a
7	BATF	chr2:53161603-53162043	GM12878	blood:	n/a	chr2:53161802-53161813 chr2:53161799-53161809 chr2:53161784-53161795
8	BCL11A	chr2:53158346-53158507	GM12878	blood:	n/a	n/a
9	BCL11A	chr2:53161550-53162089	GM12878	blood:	n/a	chr2:53161787-53161796 chr2:53161788-53161797 chr2:53161801-53161810 chr2:53161802-53161811
10	BCL11A	chr2:53161743-53162072	GM12878	blood:	n/a	chr2:53161787-53161796 chr2:53161788-53161797 chr2:53161801-53161810 chr2:53161802-53161811
11	BCL11A	chr2:53152851-53153076	GM12878	blood:	n/a	n/a
12	BCL11A	chr2:53166415-53166672	GM12878	blood:	n/a	n/a
13	BCL3	chr2:53161702-53162170	GM12878	blood:	n/a	chr2:53161787-53161796 chr2:53161788-53161797 chr2:53161801-53161810 chr2:53161802-53161811
14	BHLHE40	chr2:53161740-53162175	GM12878	blood:	n/a	n/a
15	BRCA1	chr2:53160924-53162066	Hela-S3	cervix:	n/a	n/a
16	CBX3	chr2:53161275-53162160	HCT-116	colon:	n/a	n/a
17	CBX3	chr2:53161249-53162217	HCT-116	colon:	n/a	chr2:53162199-53162210
18	CEBPB	chr2:53161347-53161796	A549	lung:	n/a	chr2:53161529-53161540 chr2:53161549-53161560
19	CEBPB	chr2:53161204-53162173	HCT-116	colon:	n/a	chr2:53161529-53161540 chr2:53161549-53161560 chr2:53161857-53161869
20	CEBPB	chr2:53161220-53162079	IMR90	lung:	n/a	chr2:53161529-53161540 chr2:53161549-53161560 chr2:53161857-53161869
21	CEBPB	chr2:53161558-53162223	GM12878	blood:	n/a	chr2:53161857-53161869
22	CEBPB	chr2:53131724-53132020	MCF-7	breast:	n/a	chr2:53131973-53131984
23	CEBPB	chr2:53161386-53161765	ECC-1	luminal epithelium:	n/a	chr2:53161529-53161540 chr2:53161549-53161560
24	CEBPB	chr2:53155376-53155506	A549	lung:	n/a	n/a
25	CEBPB	chr2:53161266-53162009	A549	lung:	n/a	chr2:53161529-53161540 chr2:53161549-53161560 chr2:53161857-53161869
26	CEBPB	chr2:53161364-53161728	HepG2	liver:	n/a	chr2:53161529-53161540 chr2:53161549-53161560
27	CEBPB	chr2:53161339-53161782	ECC-1	luminal epithelium:	n/a	chr2:53161529-53161540 chr2:53161549-53161560
28	CEBPB	chr2:53160531-53162111	Hela-S3	cervix:	n/a	chr2:53161529-53161540 chr2:53161549-53161560 chr2:53161857-53161869
29	CEBPB	chr2:53145642-53146180	IMR90	lung:	n/a	chr2:53145956-53145969
30	CEBPB	chr2:53161430-53161743	MCF-7	breast:	n/a	chr2:53161529-53161540 chr2:53161549-53161560
31	CEBPB	chr2:53145768-53146137	Hela-S3	cervix:	n/a	chr2:53145956-53145969
32	CEBPB	chr2:53160427-53162176	HCT-116	colon:	n/a	chr2:53161529-53161540 chr2:53161549-53161560 chr2:53161857-53161869
33	CEBPB	chr2:53161361-53161813	A549	lung:	n/a	chr2:53161529-53161540 chr2:53161549-53161560
34	CEBPB	chr2:53131722-53132000	Hela-S3	cervix:	n/a	chr2:53131973-53131984
35	CHD2	chr2:53161471-53162033	Hela-S3	cervix:	n/a	n/a
36	CHD2	chr2:53158847-53159196	GM12878	blood:	n/a	n/a
37	CHD2	chr2:53161727-53162018	GM12878	blood:	n/a	n/a
38	CHD2	chr2:53163995-53164008	GM12878	blood:	n/a	n/a
39	CREB1	chr2:53161602-53162274	GM12878	blood:	n/a	n/a
40	CTCF	chr2:53152810-53153082	A549	lung:	n/a	n/a
41	CTCF	chr2:53158397-53158441	GM13976	blood:	n/a	n/a
42	CTCF	chr2:53160540-53160690	HPF	lung:	n/a	n/a
43	CTCF	chr2:53157556-53157611	GM13976	blood:	n/a	n/a
44	CTCF	chr2:53157575-53157704	Lung_OC	lung:	n/a	n/a
45	CUX1	chr2:53161485-53162120	GM12878	blood:	n/a	n/a
46	E2F4	chr2:53145806-53146165	MCF10A-Er-Src	breast:	n/a	n/a
47	E2F4	chr2:53161583-53162045	MCF10A-Er-Src	breast:	n/a	n/a
48	EBF1	chr2:53162351-53162828	GM12878	blood:	n/a	n/a
49	EBF1	chr2:53161641-53162126	GM12878	blood:	n/a	n/a
50	EBF1	chr2:53158099-53158304	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:53160678-53160728	Jurkat	blood:	n/a
2	chr2:53160678-53160728	Jurkat	blood:	n/a
3	chr2:53160678-53160728	HCPEpiC	choroid plexus:	n/a
4	chr2:53160678-53160728	PFSK-1	brain:	n/a
5	chr2:53160678-53160728	Caco-2	colon:	n/a
6	chr2:53160678-53160728	HEK293	kidney:	embryo
7	chr2:53160678-53160728	GM12891	blood:	n/a
8	chr2:53160678-53160728	HUVEC	blood vessel:	n/a
9	chr2:53160678-53160728	AG10803	skin:	n/a
10	chr2:53160678-53160728	AG04450	lung:	fetal
11	chr2:53160678-53160728	A549	lung:	n/a
12	chr2:53160678-53160728	HIPEpiC	eye:	n/a
13	chr2:53160678-53160728	HCM	heart:	n/a
14	chr2:53160678-53160728	HMEC	breast:	n/a
15	chr2:53160678-53160728	NB4	blood:	n/a
16	chr2:53160678-53160728	BE2_C	brain:	n/a
17	chr2:53160678-53160728	GM12878	blood:	n/a
18	chr2:53160678-53160728	BJ	skin:	n/a
19	chr2:53160678-53160728	SAEC	small airway:	n/a
20	chr2:53160678-53160728	SK-N-SH_RA	brain:	n/a
21	chr2:53160678-53160728	HRE	kidney:	n/a
22	chr2:53160678-53160728	HL-60	blood:	n/a
23	chr2:53160678-53160728	GM06990	blood:	n/a
24	chr2:53160678-53160728	HNPCEpiC	eye:	n/a
25	chr2:53160678-53160728	K562	blood:	n/a
26	chr2:53160678-53160728	NHBE	bronchial:	n/a
27	chr2:53160678-53160728	MCF-7	breast:	n/a
28	chr2:53160678-53160728	Hepatocyte	liver:	n/a
29	chr2:53160678-53160728	AoSMC	blood vessel:	n/a
30	chr2:53160678-53160728	NT2-D1	testis:	n/a
31	chr2:53160678-53160728	GM12892	blood:	n/a
32	chr2:53160678-53160728	HRPEpiC	eye:	n/a
33	chr2:53160678-53160728	ovcar-3	ovarian:	n/a
34	chr2:53160678-53160728	LNCaP	prostate:	n/a
35	chr2:53160678-53160728	MCF10A-Er-Src	breast:	n/a
36	chr2:53160678-53160728	HRCEpiC	kidney:	n/a
37	chr2:53160678-53160728	NHDF-neo	bronchial:	n/a
38	chr2:53160678-53160728	HAEpiC	amniotic membrane:	n/a
39	chr2:53160678-53160728	SKMC	muscle:	n/a
40	chr2:53160678-53160728	SK-N-SH	brain:	n/a
41	chr2:53160678-53160728	T-47D	breast:	n/a
42	chr2:53160678-53160728	HEEpiC	esophagus:	n/a
43	chr2:53160678-53160728	AG09309	skin:	n/a
44	chr2:53160678-53160728	U87	brain:	n/a
45	chr2:53160678-53160728	Hela-S3	cervix:	n/a
46	chr2:53160678-53160728	RPTEC	kidney:	n/a
47	chr2:53160678-53160728	HPAEpiC	pulmonary alveolar:	n/a
48	chr2:53160678-53160728	HCF	heart:	n/a
49	chr2:53160678-53160728	H1-hESC	embryonic stem cell:	embryo
50	chr2:53160678-53160728	ECC-1	luminal epithelium:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53132852..53133808-chr20:52198265..52198765,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASB3-1	chr2:53137102-53137158	ENSG00000228033
2	lnc-ASB3-1	chr2:53137102-53137158	ENSG00000228033

Variant related genes	Relation type
ENSG00000228033	TF binding region
ENSG00000228033	CpG island

Extended variants
information (count: 1993 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:1993 , 50 per page) page: 1 2 3 4 5 6 7 ... 40

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs78766470	chr2:53129701-53129702	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs114453500	chr2:53129702-53129703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs56357423	chr2:53129718-53129719	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs572538533	chr2:53129719-53129720	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs535006975	chr2:53129727-53129728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs555049023	chr2:53129764-53129765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs575139461	chr2:53129787-53129788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs557266834	chr2:53129789-53129790	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs544137312	chr2:53129791-53129792	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs187876767	chr2:53129795-53129796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs13014773	chr2:53129815-53129816	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs546403951	chr2:53129843-53129844	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs564811386	chr2:53129865-53129866	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs527418969	chr2:53129888-53129889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs140759671	chr2:53129890-53129891	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs560563708	chr2:53129939-53129940	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs199986842	chr2:53130031-53130032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs529907376	chr2:53130071-53130072	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs368201430	chr2:53130080-53130081	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs549687832	chr2:53130082-53130083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs569963454	chr2:53130091-53130092	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs538440385	chr2:53130113-53130114	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs552391290	chr2:53130121-53130122	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs193140228	chr2:53130141-53130142	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs539694413	chr2:53130204-53130205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs372467853	chr2:53130205-53130206	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs554961444	chr2:53130223-53130224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs376715565	chr2:53130264-53130265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs537711524	chr2:53130265-53130266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs374889720	chr2:53130276-53130277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs79529481	chr2:53130285-53130286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs114494596	chr2:53130291-53130292	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs577498692	chr2:53130324-53130325	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs201220044	chr2:53130336-53130337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs144599929	chr2:53130344-53130345	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs541139635	chr2:53130362-53130363	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs373750287	chr2:53130367-53130368	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs571770081	chr2:53130372-53130373	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs35621438	chr2:53130376-53130377	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs62140277	chr2:53130402-53130403	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs529623282	chr2:53130428-53130429	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs116237821	chr2:53130441-53130442	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs563425719	chr2:53130478-53130479	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs17043743	chr2:53130541-53130542	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs552040395	chr2:53130550-53130551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs565875765	chr2:53130584-53130585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs377165992	chr2:53130612-53130613	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs528560335	chr2:53130693-53130694	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs548721147	chr2:53130697-53130698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs185219265	chr2:53130708-53130709	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53109400-53145600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:53131400-53131800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:53131400-53132000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:53131400-53132000	Enhancers	Fetal Muscle Leg	muscle
5	chr2:53131400-53132400	Enhancers	Hela-S3	cervix
6	chr2:53144200-53144400	Enhancers	Fetal Intestine Large	intestine
7	chr2:53144200-53144400	Enhancers	Hela-S3	cervix
8	chr2:53144400-53145400	Weak transcription	Hela-S3	cervix
9	chr2:53145400-53146000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:53145400-53147000	Enhancers	Hela-S3	cervix
11	chr2:53145400-53147200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:53145400-53147200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:53145600-53146200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:53145600-53146400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:53145600-53147200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:53146400-53147200	Enhancers	Fetal Intestine Small	intestine
17	chr2:53146400-53148000	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr2:53146400-53160000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:53146800-53147000	Enhancers	Fetal Intestine Large	intestine
20	chr2:53147000-53147600	Enhancers	Stomach Mucosa	stomach
21	chr2:53156600-53157400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:53157200-53157800	Weak transcription	Aorta	Aorta
23	chr2:53157400-53158600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:53158600-53159200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:53158600-53159200	Enhancers	GM12878-XiMat	blood
26	chr2:53158800-53159200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:53159200-53160000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:53159200-53160400	Weak transcription	GM12878-XiMat	blood
29	chr2:53159200-53162200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:53160000-53160200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:53160000-53160800	Enhancers	HMEC	breast
32	chr2:53160000-53161000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:53160200-53161400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr2:53160200-53161800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:53160200-53163200	Enhancers	Hela-S3	cervix
36	chr2:53160400-53160600	Enhancers	GM12878-XiMat	blood
37	chr2:53160600-53160800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:53160600-53161000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:53160600-53161000	Weak transcription	GM12878-XiMat	blood
40	chr2:53160600-53162600	Enhancers	NH-A	brain
41	chr2:53160600-53162800	Enhancers	Osteobl	bone
42	chr2:53160800-53161200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:53160800-53161200	Enhancers	A549	lung
44	chr2:53160800-53161400	Enhancers	Fetal Intestine Small	intestine
45	chr2:53160800-53161600	Flanking Active TSS	HMEC	breast
46	chr2:53161000-53161200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:53161000-53161200	Enhancers	Fetal Intestine Large	intestine
48	chr2:53161000-53161400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:53161000-53161800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:53161000-53161800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links