Variant report

Variant	nsv569606
Chromosome Location	chr15:59883809-59894636
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	chr15:59886705-59887063	HepG2	liver:	n/a	n/a
2	ATF1	chr15:59883692-59883919	K562	blood:	n/a	n/a
3	ATF3	chr15:59886536-59887289	A549	lung:	n/a	n/a
4	ATF3	chr15:59886503-59887273	A549	lung:	n/a	n/a
5	BCL3	chr15:59886516-59887297	A549	lung:	n/a	chr15:59886977-59886986
6	BCL3	chr15:59886506-59887541	A549	lung:	n/a	chr15:59886977-59886986 chr15:59886512-59886521
7	BRCA1	chr15:59887152-59887159	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr15:59886402-59887459	A549	lung:	n/a	n/a
9	CEBPB	chr15:59886633-59887032	A549	lung:	n/a	n/a
10	CEBPB	chr15:59886575-59887092	A549	lung:	n/a	n/a
11	CREB1	chr15:59886682-59887155	A549	lung:	n/a	n/a
12	CREB1	chr15:59887459-59887957	A549	lung:	n/a	n/a
13	CTCF	chr15:59891840-59891990	HepG2	liver:	n/a	n/a
14	E2F4	chr15:59886452-59886652	MCF10A-Er-Src	breast:	n/a	n/a
15	ELF1	chr15:59887587-59888159	HepG2	liver:	n/a	n/a
16	ELF1	chr15:59886632-59887175	A549	lung:	n/a	n/a
17	ELF1	chr15:59887572-59888113	HepG2	liver:	n/a	n/a
18	EP300	chr15:59886471-59888087	A549	lung:	n/a	n/a
19	EP300	chr15:59886642-59887080	HepG2	liver:	n/a	n/a
20	EP300	chr15:59887585-59888164	HepG2	liver:	n/a	n/a
21	EP300	chr15:59888660-59888796	HepG2	liver:	n/a	n/a
22	EP300	chr15:59886755-59887064	HepG2	liver:	n/a	n/a
23	EP300	chr15:59886731-59887091	HepG2	liver:	n/a	n/a
24	EP300	chr15:59886370-59888218	A549	lung:	n/a	n/a
25	FOS	chr15:59886568-59886868	MCF10A-Er-Src	breast:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886720 chr15:59886709-59886716
26	FOS	chr15:59886559-59886843	MCF10A-Er-Src	breast:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886720 chr15:59886709-59886716
27	FOS	chr15:59886531-59886861	MCF10A-Er-Src	breast:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886720 chr15:59886709-59886716
28	FOS	chr15:59886558-59886796	HUVEC	blood vessel:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886720 chr15:59886709-59886716
29	FOS	chr15:59886560-59886889	MCF10A-Er-Src	breast:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886720 chr15:59886709-59886716
30	FOSL2	chr15:59886498-59887209	A549	lung:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886716
31	FOSL2	chr15:59886302-59887391	A549	lung:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886716
32	FOXA1	chr15:59887770-59888098	HepG2	liver:	n/a	n/a
33	FOXA1	chr15:59886640-59886999	T-47D	breast:	n/a	n/a
34	FOXA1	chr15:59887648-59888101	HepG2	liver:	n/a	n/a
35	FOXA1	chr15:59886702-59887047	HepG2	liver:	n/a	n/a
36	FOXA1	chr15:59887717-59888150	HepG2	liver:	n/a	n/a
37	FOXA2	chr15:59886346-59887115	A549	lung:	n/a	n/a
38	FOXA2	chr15:59886654-59886978	HepG2	liver:	n/a	n/a
39	FOXA2	chr15:59887745-59888126	HepG2	liver:	n/a	n/a
40	FOXA2	chr15:59886535-59887210	A549	lung:	n/a	n/a
41	GABPA	chr15:59886568-59887115	A549	lung:	n/a	n/a
42	GATA3	chr15:59886400-59888118	A549	lung:	n/a	chr15:59886709-59886718
43	GATA3	chr15:59886706-59887070	T-47D	breast:	n/a	chr15:59886709-59886718
44	GATA3	chr15:59886681-59887155	T-47D	breast:	n/a	chr15:59886709-59886718
45	HDAC2	chr15:59887614-59888092	HepG2	liver:	n/a	chr15:59887836-59887844
46	HNF4A	chr15:59887653-59888149	HepG2	liver:	n/a	chr15:59887837-59887845 chr15:59887831-59887843 chr15:59887956-59887964 chr15:59887836-59887844 chr15:59887766-59887778 chr15:59887829-59887844 chr15:59887838-59887846
47	HNF4A	chr15:59887663-59888028	HepG2	liver:	n/a	chr15:59887837-59887845 chr15:59887831-59887843 chr15:59887956-59887964 chr15:59887836-59887844 chr15:59887766-59887778 chr15:59887829-59887844 chr15:59887838-59887846
48	HNF4G	chr15:59887628-59888022	HepG2	liver:	n/a	chr15:59887837-59887845 chr15:59887831-59887843 chr15:59887956-59887964 chr15:59887836-59887844 chr15:59887828-59887843 chr15:59887766-59887778 chr15:59887838-59887846
49	IKZF1	chr15:59883598-59883935	GM12878	blood:	n/a	n/a
50	JUN	chr15:59886554-59887026	HepG2	liver:	n/a	chr15:59886707-59886718 chr15:59886711-59886720 chr15:59886709-59886716

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59891996..59893878-chr15:59903015..59905190,2	K562	blood:
2	chr15:59891038..59893878-chr15:59903015..59906504,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCNT3-2	chr15:59891852-59891910	NONHSAT044181
2	lnc-GCNT3-2	chr15:59888442-59888553	NONHSAT044179
3	lnc-GCNT3-2	chr15:59887928-59888112	NONHSAT044179
4	lnc-GCNT3-2	chr15:59887074-59887113	NONHSAT044178
5	lnc-GCNT3-2	chr15:59888493-59888553	NONHSAT044178
6	lnc-GCNT3-2	chr15:59891842-59891910	NONHSAT044180

Variant related genes	Relation type
GCNT3	TF binding region
ENSG00000140297	chromatin interactions

Extended variants
information (count: 632 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:632 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7179783	chr15:59883809-59883810	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs535754632	chr15:59883842-59883843	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs146910714	chr15:59883862-59883863	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs370930210	chr15:59883892-59883893	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs565855822	chr15:59883946-59883947	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs10163153	chr15:59883966-59883967	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs191986403	chr15:59883969-59883970	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs16941501	chr15:59883982-59883983	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs543803337	chr15:59884058-59884059	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs547987324	chr15:59884065-59884066	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs12440292	chr15:59884098-59884099	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs527907248	chr15:59884119-59884120	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs75949178	chr15:59884120-59884121	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs74019636	chr15:59884138-59884139	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs182850667	chr15:59884148-59884149	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs562233890	chr15:59884163-59884164	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs545226309	chr15:59884168-59884169	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs141764120	chr15:59884202-59884203	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs143786493	chr15:59884209-59884210	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs549328391	chr15:59884210-59884211	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs148219500	chr15:59884211-59884212	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs528919221	chr15:59884245-59884246	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs547651881	chr15:59884246-59884247	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs187701855	chr15:59884264-59884265	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs72751123	chr15:59884299-59884300	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs192885440	chr15:59884301-59884302	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs141219942	chr15:59884313-59884314	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs150287852	chr15:59884320-59884321	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs555627539	chr15:59884322-59884323	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs368155290	chr15:59884326-59884327	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs546273985	chr15:59884342-59884343	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs536119316	chr15:59884345-59884346	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs184039828	chr15:59884358-59884359	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs187255943	chr15:59884359-59884360	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs16941503	chr15:59884369-59884370	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs563552071	chr15:59884402-59884403	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs553798625	chr15:59884428-59884429	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs200442424	chr15:59884429-59884430	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs375549948	chr15:59884440-59884441	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs143745186	chr15:59884441-59884442	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs71119488	chr15:59884442-59884443	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs57501848	chr15:59884443-59884444	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs552006415	chr15:59884455-59884456	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs137894502	chr15:59884483-59884484	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs543491975	chr15:59884525-59884526	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs142617247	chr15:59884534-59884535	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs146033328	chr15:59884579-59884580	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs191968327	chr15:59884597-59884598	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs561412800	chr15:59884630-59884631	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs377236305	chr15:59884633-59884634	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Testicular germ cell tumor	18059402	CNVD
cataract	16735990	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Medulloblastoma	21979893	CNVD
spastic paraplegia with thinning of corpus callosum	19105190	CNVD
Schizophrenia	21324950	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Disease	21824424	CNVD
Melanoma	18172304	CNVD
Gastric cancer	17167181	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Colorectal cancer	16272173	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Multiple myeloma	17550852	CNVD
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Prostate cancer	16573809	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Lung cancer	18438408	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	17053054	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Cancer	21129771	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Abnormal phenotypes	18644119	CNVD
Cancer	16751803	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital diaphragmatic hernia	21341218	CNVD
Holoprosencephaly	21359414	CNVD
Myelofibrosis	22110671	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Mental retardation	17124404	CNVD
Gastrointestinal stromal cancer	20877625	CNVD

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59880000-59884000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:59882400-59884200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr15:59882400-59891600	Weak transcription	Small Intestine	intestine
4	chr15:59882600-59884200	Enhancers	GM12878-XiMat	blood
5	chr15:59883000-59884200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr15:59883000-59884400	Enhancers	Duodenum Mucosa	Duodenum
7	chr15:59883200-59884200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:59883200-59884200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr15:59883200-59884200	Enhancers	Fetal Intestine Small	intestine
10	chr15:59883200-59884200	Enhancers	Stomach Mucosa	stomach
11	chr15:59883200-59884400	Enhancers	Fetal Intestine Large	intestine
12	chr15:59883200-59884600	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr15:59883200-59884600	Enhancers	NHEK	skin
14	chr15:59883400-59884200	Enhancers	A549	lung
15	chr15:59883400-59884600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:59883600-59884200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:59883600-59884200	Enhancers	Fetal Heart	heart
18	chr15:59883600-59884400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:59883600-59884400	Enhancers	HMEC	breast
20	chr15:59883600-59887200	Weak transcription	Colonic Mucosa	Colon
21	chr15:59883800-59884200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:59883800-59884200	Enhancers	HepG2	liver
23	chr15:59883800-59887400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:59884000-59884600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:59884200-59885400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:59884200-59886000	Weak transcription	Fetal Intestine Small	intestine
27	chr15:59884200-59886000	Weak transcription	A549	lung
28	chr15:59884200-59886400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:59884200-59886400	Weak transcription	HepG2	liver
30	chr15:59884200-59886600	Weak transcription	Stomach Mucosa	stomach
31	chr15:59884400-59885400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:59884400-59885600	Weak transcription	Fetal Intestine Large	intestine
33	chr15:59884400-59886800	Weak transcription	HMEC	breast
34	chr15:59884400-59887000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:59884600-59884800	Enhancers	Esophagus	oesophagus
36	chr15:59884600-59885400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:59884600-59886400	Weak transcription	NHEK	skin
38	chr15:59884600-59886600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:59884800-59886800	Weak transcription	Esophagus	oesophagus
40	chr15:59885400-59887200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr15:59885400-59887800	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr15:59885400-59888000	Enhancers	Duodenum Mucosa	Duodenum
43	chr15:59885600-59886200	Enhancers	Fetal Intestine Large	intestine
44	chr15:59885600-59886400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:59886000-59886200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr15:59886000-59886400	Enhancers	A549	lung
47	chr15:59886000-59889400	Enhancers	Fetal Intestine Small	intestine
48	chr15:59886200-59886800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:59886200-59886800	Weak transcription	Fetal Intestine Large	intestine
50	chr15:59886400-59886800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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