Variant report

Variant	esv3358006
Chromosome Location	chr2:53108148-53112546
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	BCL3	chr2:53108842-53109038	GM12878	blood:	n/a	chr2:53108968-53108977
2	CBX3	chr2:53108658-53109304	HCT-116	colon:	n/a	n/a
3	CEBPB	chr2:53108848-53109174	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr2:53108744-53109210	IMR90	lung:	n/a	n/a
5	CEBPB	chr2:53108693-53109318	HCT-116	colon:	n/a	n/a
6	E2F4	chr2:53108919-53109431	MCF10A-Er-Src	breast:	n/a	n/a
7	EBF1	chr2:53108199-53108282	GM12878	blood:	n/a	n/a
8	EBF1	chr2:53108700-53108950	GM12878	blood:	n/a	chr2:53108820-53108830 chr2:53108819-53108830 chr2:53108820-53108829
9	EP300	chr2:53108704-53109309	A549	lung:	n/a	n/a
10	FOS	chr2:53108790-53109147	MCF10A-Er-Src	breast:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
11	FOS	chr2:53108793-53109128	MCF10A-Er-Src	breast:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
12	FOS	chr2:53108786-53109176	MCF10A-Er-Src	breast:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
13	FOS	chr2:53108173-53108381	MCF10A-Er-Src	breast:	n/a	chr2:53108299-53108309 chr2:53108301-53108308 chr2:53108300-53108308 chr2:53108344-53108353
14	FOS	chr2:53108788-53109130	MCF10A-Er-Src	breast:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
15	FOSL1	chr2:53108676-53109299	HCT-116	colon:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
16	FOSL2	chr2:53108679-53109166	A549	lung:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
17	FOSL2	chr2:53108797-53109105	A549	lung:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
18	FOXA1	chr2:53108628-53109134	A549	lung:	n/a	n/a
19	FOXA2	chr2:53108763-53109170	A549	lung:	n/a	n/a
20	GATA3	chr2:53108709-53109172	MCF-7	breast:	n/a	chr2:53108967-53108976
21	JUND	chr2:53108787-53109287	HCT-116	colon:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
22	JUND	chr2:53108716-53109280	HCT-116	colon:	n/a	chr2:53108967-53108978 chr2:53108969-53108977
23	JUND	chr2:53108157-53108359	HepG2	liver:	n/a	chr2:53108298-53108309 chr2:53108299-53108309 chr2:53108301-53108308 chr2:53108300-53108308 chr2:53108344-53108353
24	MAFK	chr2:53108779-53109121	IMR90	lung:	n/a	n/a
25	MAX	chr2:53108846-53109168	Hela-S3	cervix:	n/a	chr2:53108969-53108978
26	MAX	chr2:53112406-53112409	GM12878	blood:	n/a	n/a
27	MAX	chr2:53109222-53109539	NB4	blood:	n/a	chr2:53109368-53109375 chr2:53109368-53109377 chr2:53109367-53109376 chr2:53109366-53109379 chr2:53109367-53109378
28	MAZ	chr2:53110054-53110064	Hela-S3	cervix:	n/a	n/a
29	MYC	chr2:53108810-53109109	MCF10A-Er-Src	breast:	n/a	chr2:53108969-53108978
30	MYC	chr2:53110387-53110399	MCF-7	breast:	n/a	n/a
31	MYC	chr2:53108833-53109188	MCF10A-Er-Src	breast:	n/a	chr2:53108969-53108978
32	NR2F2	chr2:53108789-53109267	MCF-7	breast:	n/a	n/a
33	NR3C1	chr2:53108984-53109120	A549	lung:	n/a	n/a
34	NR3C1	chr2:53108823-53109168	A549	lung:	n/a	n/a
35	NR3C1	chr2:53108853-53109151	A549	lung:	n/a	n/a
36	POLR2A	chr2:53109921-53110379	A549	lung:	n/a	n/a
37	POLR2A	chr2:53108779-53109111	U87	brain:	n/a	n/a
38	POLR2A	chr2:53110489-53110509	Gliobla	brain:	n/a	n/a
39	POLR2A	chr2:53110450-53110451	Gliobla	brain:	n/a	n/a
40	POLR2A	chr2:53108779-53109131	U87	brain:	n/a	n/a
41	RCOR1	chr2:53108549-53109377	IMR90	lung:	n/a	n/a
42	SIN3AK20	chr2:53108619-53109262	MCF-7	breast:	n/a	n/a
43	SP1	chr2:53108719-53109251	A549	lung:	n/a	n/a
44	SP1	chr2:53108669-53109332	HCT-116	colon:	n/a	n/a
45	SP1	chr2:53108628-53109273	A549	lung:	n/a	n/a
46	STAT3	chr2:53108847-53109047	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr2:53108868-53109068	MCF10A-Er-Src	breast:	n/a	n/a
48	STAT3	chr2:53108845-53109085	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT3	chr2:53108853-53109095	MCF10A-Er-Src	breast:	n/a	n/a
50	TCF12	chr2:53108681-53109251	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53103066..53106486-chr2:53106611..53109718,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC2-6	chr2:53110381-53110593	NONHSAT070683

Variant related genes	Relation type
ENSG00000232668	TF binding region

Extended variants
information (count: 215 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:215 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs576115785	chr2:53108167-53108168	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs78956236	chr2:53108198-53108199	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs191595803	chr2:53108248-53108249	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs527444190	chr2:53108278-53108279	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs12713232	chr2:53108308-53108309	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs535708798	chr2:53108381-53108382	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs368539240	chr2:53108415-53108416	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs560773106	chr2:53108454-53108455	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs554644499	chr2:53108455-53108456	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs184632911	chr2:53108502-53108503	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs139022769	chr2:53108534-53108535	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs538660445	chr2:53108537-53108538	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs552810327	chr2:53108553-53108554	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs188319735	chr2:53108564-53108565	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs535364726	chr2:53108595-53108596	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs555179491	chr2:53108615-53108616	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs575133564	chr2:53108639-53108640	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs371761230	chr2:53108643-53108644	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs12990843	chr2:53108688-53108689	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs556295866	chr2:53108702-53108703	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs367832705	chr2:53108734-53108735	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs547461093	chr2:53108767-53108768	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs192170560	chr2:53108798-53108799	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs544692561	chr2:53108879-53108880	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs564927463	chr2:53108885-53108886	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs572221920	chr2:53108910-53108911	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs541360161	chr2:53108929-53108930	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs184486381	chr2:53108960-53108961	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs1864534	chr2:53109005-53109006	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs576935035	chr2:53109046-53109047	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs375783318	chr2:53109063-53109064	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs549817296	chr2:53109071-53109072	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs563465420	chr2:53109073-53109074	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs149442567	chr2:53109074-53109075	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs552273658	chr2:53109089-53109090	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs76901473	chr2:53109094-53109095	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs528778270	chr2:53109095-53109096	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs548908767	chr2:53109109-53109110	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs568622515	chr2:53109133-53109134	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs144785558	chr2:53109142-53109143	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs556259176	chr2:53109177-53109178	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs148567762	chr2:53109182-53109183	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs538752850	chr2:53109221-53109222	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs372261342	chr2:53109232-53109233	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs546096935	chr2:53109248-53109249	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs558261497	chr2:53109256-53109257	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs113203918	chr2:53109261-53109262	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs540889326	chr2:53109262-53109263	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs554449688	chr2:53109298-53109299	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs113663199	chr2:53109300-53109301	Weak transcription Enhancers	TF binding region	1 gene(s)	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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53094400-53108600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:53102600-53108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:53105600-53108200	Weak transcription	A549	lung
4	chr2:53105600-53121800	Weak transcription	Pancreas	Pancrea
5	chr2:53107200-53109000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:53107600-53108200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:53107600-53108200	Enhancers	Fetal Heart	heart
8	chr2:53107600-53109000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:53107800-53109000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:53107800-53109200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:53108200-53108400	Enhancers	A549	lung
12	chr2:53108200-53109200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:53108200-53119800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:53108400-53108800	Weak transcription	A549	lung
15	chr2:53108600-53109400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:53108600-53109400	Enhancers	Hela-S3	cervix
17	chr2:53108800-53109200	Enhancers	A549	lung
18	chr2:53108800-53109600	Enhancers	HMEC	breast
19	chr2:53109000-53109200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:53109200-53110400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:53109200-53115800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:53109400-53145600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:53110200-53110400	Enhancers	Gastric	stomach
24	chr2:53110400-53110600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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