Variant report

Variant	nsv569518
Chromosome Location	chr15:54898631-54954864
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	chr15:54909959-54910868	HepG2	liver:	n/a	n/a
2	BATF	chr15:54908894-54909106	GM12878	blood:	n/a	chr15:54909011-54909022
3	BHLHE40	chr15:54913156-54913250	GM12878	blood:	n/a	n/a
4	BHLHE40	chr15:54909020-54909028	GM12878	blood:	n/a	n/a
5	CEBPB	chr15:54912045-54912305	HepG2	liver:	n/a	chr15:54912151-54912162 chr15:54912150-54912163
6	CEBPB	chr15:54953018-54953270	HepG2	liver:	n/a	chr15:54953129-54953140
7	CEBPB	chr15:54910340-54910679	HepG2	liver:	n/a	n/a
8	CEBPB	chr15:54933955-54934258	HepG2	liver:	n/a	chr15:54934095-54934106
9	CEBPB	chr15:54933930-54934219	A549	lung:	n/a	chr15:54934095-54934106
10	CEBPB	chr15:54933917-54934156	K562	blood:	n/a	chr15:54934095-54934106
11	CEBPB	chr15:54910450-54910580	HepG2	liver:	n/a	n/a
12	CEBPB	chr15:54933938-54934258	IMR90	lung:	n/a	chr15:54934095-54934106
13	CTCF	chr15:54937796-54937988	GM12878	blood:	n/a	n/a
14	CTCF	chr15:54937817-54937858	GM12878	blood:	n/a	n/a
15	CTCF	chr15:54937680-54937830	RPTEC	kidney:	n/a	n/a
16	CTCF	chr15:54937787-54937896	LNCaP	prostate:	n/a	n/a
17	CTCF	chr15:54952751-54952795	GM13976	blood:	n/a	n/a
18	CTCF	chr15:54937800-54937950	GM06990	blood:	n/a	n/a
19	CTCF	chr15:54937760-54937910	RPTEC	kidney:	n/a	n/a
20	CTCF	chr15:54937774-54937878	HepG2	liver:	n/a	n/a
21	CTCF	chr15:54902511-54902544	GM20000	blood:	n/a	n/a
22	CTCF	chr15:54898985-54899060	Lung_OC	lung:	n/a	n/a
23	CTCF	chr15:54937860-54938010	GM06990	blood:	n/a	n/a
24	CUX1	chr15:54914977-54915129	GM12878	blood:	n/a	n/a
25	E2F4	chr15:54908178-54908378	MCF10A-Er-Src	breast:	n/a	n/a
26	EBF1	chr15:54906039-54906410	GM12878	blood:	n/a	chr15:54906222-54906233
27	EBF1	chr15:54910441-54910543	GM12878	blood:	n/a	n/a
28	EP300	chr15:54910321-54910772	HepG2	liver:	n/a	chr15:54910377-54910386
29	EP300	chr15:54910277-54910629	HepG2	liver:	n/a	chr15:54910377-54910386
30	EP300	chr15:54908995-54909081	GM12878	blood:	n/a	n/a
31	EP300	chr15:54911833-54911840	GM12878	blood:	n/a	n/a
32	EP300	chr15:54911380-54911684	HepG2	liver:	n/a	n/a
33	FAM48A	chr15:54922904-54923041	GM12878	blood:	n/a	n/a
34	FOS	chr15:54951898-54952074	MCF10A-Er-Src	breast:	n/a	chr15:54951979-54951986 chr15:54951978-54951987 chr15:54951978-54951986 chr15:54951977-54951986
35	FOS	chr15:54952658-54952906	MCF10A-Er-Src	breast:	n/a	chr15:54952740-54952748 chr15:54952740-54952747
36	FOSL2	chr15:54910297-54910610	HepG2	liver:	n/a	n/a
37	FOXA1	chr15:54910179-54910681	HepG2	liver:	n/a	n/a
38	FOXA1	chr15:54910273-54910644	HepG2	liver:	n/a	n/a
39	FOXA1	chr15:54910234-54910610	HepG2	liver:	n/a	n/a
40	FOXA1	chr15:54919138-54919515	T-47D	breast:	n/a	n/a
41	FOXA1	chr15:54919134-54919460	T-47D	breast:	n/a	n/a
42	FOXA1	chr15:54911276-54911742	HepG2	liver:	n/a	n/a
43	FOXA1	chr15:54911389-54911681	HepG2	liver:	n/a	n/a
44	FOXA1	chr15:54910261-54910644	HepG2	liver:	n/a	n/a
45	FOXA2	chr15:54910264-54910615	HepG2	liver:	n/a	n/a
46	FOXA2	chr15:54911380-54911703	HepG2	liver:	n/a	n/a
47	GATA3	chr15:54919118-54919482	T-47D	breast:	n/a	n/a
48	GATA3	chr15:54919076-54919499	T-47D	breast:	n/a	n/a
49	GATA3	chr15:54900401-54900711	T-47D	breast:	n/a	n/a
50	HNF4G	chr15:54911396-54911576	HepG2	liver:	n/a	chr15:54911505-54911520

No.	Distal block	Cell Line	Cell type
1	chr15:54926871..54929608-chr15:54933305..54935449,2	K562	blood:
2	chr15:54926871..54929608-chr15:54933305..54935449,2	K562	blood:
3	chr15:54910155..54912492-chr15:54912771..54915484,2	MCF-7	breast:
4	chr15:54910155..54912492-chr15:54912771..54915484,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSL24D1-4	chr15:54902051-54903329	NONHSAT043976

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	UNC13C	hsa-miR-128-3p	chr15:54919866-54919886
2	UNC13C	hsa-miR-128-3p	chr15:54919879-54919886

Variant related genes	Relation type
UNC13C	TF binding region

Extended variants
information (count: 1560 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:1560 , 50 per page) page: 1 2 3 4 5 6 7 ... 32

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9284299	chr15:54898631-54898632	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs190690061	chr15:54898701-54898702	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs574882608	chr15:54898720-54898721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs113589384	chr15:54898725-54898726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs144898284	chr15:54898748-54898749	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs563815404	chr15:54898834-54898835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs79193053	chr15:54898837-54898838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs546393370	chr15:54898885-54898886	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs182109694	chr15:54898903-54898904	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs186705284	chr15:54898932-54898933	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs79659196	chr15:54898941-54898942	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs569486236	chr15:54898943-54898944	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs192337369	chr15:54898965-54898966	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs116316186	chr15:54899030-54899031	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs571686328	chr15:54899031-54899032	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs115648819	chr15:54899092-54899093	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs553980637	chr15:54899098-54899099	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs572993538	chr15:54899127-54899128	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs147934278	chr15:54899184-54899185	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs184708414	chr15:54899216-54899217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs575188274	chr15:54899224-54899225	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs528698683	chr15:54899230-54899231	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs72740036	chr15:54899241-54899242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs543243116	chr15:54899247-54899248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs571869494	chr15:54899252-54899253	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs2250283	chr15:54899264-54899265	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs577227759	chr15:54899283-54899284	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs540320012	chr15:54899293-54899294	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs560030677	chr15:54899316-54899317	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs55709902	chr15:54899339-54899340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs549339052	chr15:54899341-54899342	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs369247224	chr15:54899359-54899360	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs143723373	chr15:54899389-54899390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs112429294	chr15:54899435-54899436	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs374447868	chr15:54899454-54899455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs552109492	chr15:54899625-54899626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs571624955	chr15:54899640-54899641	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs542330466	chr15:54899663-54899664	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs115626175	chr15:54899690-54899691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs547862150	chr15:54899736-54899737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs567691121	chr15:54899758-54899759	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs148112235	chr15:54899766-54899767	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs188354871	chr15:54899770-54899771	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs565093122	chr15:54899823-54899824	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs555244038	chr15:54899849-54899850	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs575113176	chr15:54899946-54899947	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs537707716	chr15:54899951-54899952	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs80212747	chr15:54899971-54899972	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs375052473	chr15:54899982-54899983	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs140957086	chr15:54900021-54900022	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
Colorectal cancer	16774939	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
Chronic lymphocytic leukemia	21546498	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	17053054	CNVD
Breast cancer	22032731	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Hirschsprung''s Disease	21712996	CNVD
Myeloproliferative neoplasm	20015882	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
Myelofibrosis	22110671	CNVD
Acute monocytic leukemia	16498392	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cancer	17440070	CNVD

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54896800-54899800	Weak transcription	Aorta	Aorta
2	chr15:54897800-54899000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:54898200-54899800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:54898600-54899800	Weak transcription	Fetal Lung	lung
5	chr15:54899000-54899200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:54899800-54900000	Enhancers	Aorta	Aorta
7	chr15:54899800-54900200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr15:54899800-54901600	Enhancers	Fetal Lung	lung
9	chr15:54900000-54920600	Weak transcription	Aorta	Aorta
10	chr15:54900200-54901200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:54901000-54902200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:54901200-54901400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr15:54901200-54902200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:54906000-54906200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:54906200-54910000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:54906400-54916000	Weak transcription	Fetal Lung	lung
17	chr15:54907400-54915800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr15:54909600-54911400	Enhancers	Fetal Intestine Large	intestine
19	chr15:54909800-54912400	Enhancers	HepG2	liver
20	chr15:54910000-54911000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:54910000-54913000	Enhancers	Fetal Intestine Small	intestine
22	chr15:54910200-54911000	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:54911000-54911800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:54911400-54912800	Weak transcription	Fetal Intestine Large	intestine
25	chr15:54912000-54912200	Enhancers	Duodenum Mucosa	Duodenum
26	chr15:54912800-54913200	Enhancers	Fetal Intestine Large	intestine
27	chr15:54915600-54916400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:54915800-54916000	Enhancers	Primary hematopoietic stem cells	blood
29	chr15:54916000-54916400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr15:54916000-54918000	Strong transcription	Fetal Lung	lung
31	chr15:54918000-54920400	Weak transcription	Fetal Lung	lung
32	chr15:54920400-54921400	Strong transcription	Fetal Lung	lung
33	chr15:54920600-54921400	Strong transcription	Aorta	Aorta
34	chr15:54921200-54921600	Active TSS	Gastric	stomach
35	chr15:54921400-54923000	Weak transcription	Fetal Lung	lung
36	chr15:54921400-54925400	Weak transcription	Aorta	Aorta
37	chr15:54927800-54928000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:54933000-54933400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr15:54933000-54933600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr15:54933000-54933600	Enhancers	Duodenum Mucosa	Duodenum
41	chr15:54933000-54933600	Enhancers	Fetal Intestine Large	intestine
42	chr15:54934000-54934200	Enhancers	Aorta	Aorta
43	chr15:54934200-54938000	Weak transcription	Aorta	Aorta
44	chr15:54941400-54942200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:54951400-54952000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr15:54952000-54952400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr15:54952400-54952800	Enhancers	Rectal Mucosa Donor 31	rectum

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