Variant report

Variant	nsv983993
Chromosome Location	chr15:59898156-59906382
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:95)
CpG islands
(count:123)
Chromatin interactive
region (count:3)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:95 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr15:59903791-59904170	HepG2	liver:	n/a	n/a
2	BCL3	chr15:59903393-59904359	A549	lung:	n/a	n/a
3	BHLHE40	chr15:59903850-59904160	HepG2	liver:	n/a	n/a
4	BRCA1	chr15:59903860-59904120	Hela-S3	cervix:	n/a	n/a
5	CHD2	chr15:59903849-59904022	Hela-S3	cervix:	n/a	n/a
6	CHD2	chr15:59903897-59904106	HepG2	liver:	n/a	n/a
7	CTCF	chr15:59902079-59902232	HepG2	liver:	n/a	n/a
8	CTCF	chr15:59898886-59898935	GM10266	blood:	n/a	n/a
9	CTCF	chr15:59902173-59902200	NHEK	skin:	n/a	n/a
10	CTCF	chr15:59902154-59902259	HepG2	liver:	n/a	n/a
11	ELF1	chr15:59903631-59904270	A549	lung:	n/a	n/a
12	ELK1	chr15:59904071-59904206	Hela-S3	cervix:	n/a	n/a
13	EP300	chr15:59903808-59904227	HepG2	liver:	n/a	n/a
14	EP300	chr15:59903865-59904262	HepG2	liver:	n/a	n/a
15	EP300	chr15:59903963-59904251	HepG2	liver:	n/a	n/a
16	EP300	chr15:59903437-59904482	A549	lung:	n/a	n/a
17	EP300	chr15:59903540-59904445	A549	lung:	n/a	n/a
18	ETS1	chr15:59903674-59904295	A549	lung:	n/a	chr15:59904136-59904151
19	FOS	chr15:59903843-59904186	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr15:59903872-59904160	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr15:59903855-59904176	MCF10A-Er-Src	breast:	n/a	n/a
22	FOSL2	chr15:59903638-59904267	A549	lung:	n/a	n/a
23	FOSL2	chr15:59903499-59904609	A549	lung:	n/a	n/a
24	FOSL2	chr15:59903834-59904203	HepG2	liver:	n/a	n/a
25	FOXA1	chr15:59903826-59904101	HepG2	liver:	n/a	n/a
26	FOXA1	chr15:59903761-59904104	HepG2	liver:	n/a	n/a
27	FOXA1	chr15:59903828-59904204	HepG2	liver:	n/a	n/a
28	FOXA1	chr15:59903815-59904134	HepG2	liver:	n/a	n/a
29	FOXA2	chr15:59903771-59904070	HepG2	liver:	n/a	n/a
30	FOXA2	chr15:59903833-59904261	A549	lung:	n/a	n/a
31	FOXA2	chr15:59903671-59904270	A549	lung:	n/a	n/a
32	GABPA	chr15:59903547-59904481	A549	lung:	n/a	n/a
33	GATA3	chr15:59903530-59904582	A549	lung:	n/a	n/a
34	HEY1	chr15:59903852-59904139	HepG2	liver:	n/a	n/a
35	JUN	chr15:59903859-59904083	HepG2	liver:	n/a	n/a
36	JUND	chr15:59903800-59904105	HepG2	liver:	n/a	chr15:59903978-59903989
37	JUND	chr15:59903793-59904252	A549	lung:	n/a	chr15:59903978-59903989
38	JUND	chr15:59903788-59904305	A549	lung:	n/a	chr15:59903978-59903989
39	MAFF	chr15:59903851-59904293	HepG2	liver:	n/a	chr15:59904039-59904057
40	MAFK	chr15:59903835-59904297	HepG2	liver:	n/a	chr15:59904045-59904056 chr15:59904043-59904057 chr15:59904045-59904056 chr15:59904040-59904055 chr15:59904044-59904055 chr15:59904044-59904055
41	MAFK	chr15:59903865-59904234	Hela-S3	cervix:	n/a	chr15:59904045-59904056 chr15:59904043-59904057 chr15:59904045-59904056 chr15:59904040-59904055 chr15:59904044-59904055 chr15:59904044-59904055
42	MAFK	chr15:59903787-59904226	HepG2	liver:	n/a	chr15:59904045-59904056 chr15:59904043-59904057 chr15:59904045-59904056 chr15:59904040-59904055 chr15:59904044-59904055 chr15:59904044-59904055
43	MAX	chr15:59903894-59904125	Hela-S3	cervix:	n/a	n/a
44	MAX	chr15:59903663-59904409	A549	lung:	n/a	n/a
45	MAX	chr15:59903526-59905298	A549	lung:	n/a	n/a
46	MAZ	chr15:59905000-59905161	HepG2	liver:	n/a	n/a
47	MYC	chr15:59905024-59905036	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr15:59904770-59905036	A549	lung:	n/a	n/a
49	POLR2A	chr15:59903723-59904447	HepG2	liver:	n/a	n/a
50	POLR2A	chr15:59903886-59904188	A549	lung:	n/a	n/a

(count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:59904009-59904059	ovcar-3	ovarian:	n/a
2	chr15:59904009-59904059	ovcar-3	ovarian:	n/a
3	chr15:59904009-59904059	GM12878	blood:	n/a
4	chr15:59904009-59904059	AG10803	skin:	n/a
5	chr15:59903968-59904018	SKMC	muscle:	n/a
6	chr15:59903968-59904018	CMK	blood:	n/a
7	chr15:59903968-59904018	H1-hESC	embryonic stem cell:	embryo
8	chr15:59904009-59904059	GM12892	blood:	n/a
9	chr15:59903968-59904018	NH-A	brain:	n/a
10	chr15:59904009-59904059	HRE	kidney:	n/a
11	chr15:59904009-59904059	ECC-1	luminal epithelium:	n/a
12	chr15:59903968-59904018	AG09309	skin:	n/a
13	chr15:59903968-59904018	MCF-7	breast:	n/a
14	chr15:59904009-59904059	GM06990	blood:	n/a
15	chr15:59904009-59904059	U87	brain:	n/a
16	chr15:59903968-59904018	GM12878	blood:	n/a
17	chr15:59903968-59904018	NHDF-neo	bronchial:	n/a
18	chr15:59903968-59904018	AG04449	skin:	fetal
19	chr15:59904009-59904059	Caco-2	colon:	n/a
20	chr15:59904009-59904059	SKMC	muscle:	n/a
21	chr15:59904009-59904059	HEK293	kidney:	embryo
22	chr15:59903968-59904018	GM06990	blood:	n/a
23	chr15:59904009-59904059	IMR90	lung:	fetal
24	chr15:59904009-59904059	AoSMC	blood vessel:	n/a
25	chr15:59904009-59904059	AG09309	skin:	n/a
26	chr15:59903968-59904018	Hela-S3	cervix:	n/a
27	chr15:59903968-59904018	HL-60	blood:	n/a
28	chr15:59904009-59904059	NT2-D1	testis:	n/a
29	chr15:59903968-59904018	ECC-1	luminal epithelium:	n/a
30	chr15:59903968-59904018	AG09319	gingival:	n/a
31	chr15:59904009-59904059	Hela-S3	cervix:	n/a
32	chr15:59904009-59904059	PFSK-1	brain:	n/a
33	chr15:59903968-59904018	PANC-1	pancreas:	n/a
34	chr15:59904009-59904059	HNPCEpiC	eye:	n/a
35	chr15:59904009-59904059	HCM	heart:	n/a
36	chr15:59903968-59904018	GM12891	blood:	n/a
37	chr15:59903968-59904018	K562	blood:	n/a
38	chr15:59904009-59904059	BE2_C	brain:	n/a
39	chr15:59904009-59904059	HEEpiC	esophagus:	n/a
40	chr15:59903968-59904018	HCPEpiC	choroid plexus:	n/a
41	chr15:59903968-59904018	SK-N-SH_RA	brain:	n/a
42	chr15:59904009-59904059	HUVEC	blood vessel:	n/a
43	chr15:59904009-59904059	Jurkat	blood:	n/a
44	chr15:59903968-59904018	NB4	blood:	n/a
45	chr15:59903968-59904018	PFSK-1	brain:	n/a
46	chr15:59903968-59904018	HCF	heart:	n/a
47	chr15:59903968-59904018	NT2-D1	testis:	n/a
48	chr15:59904009-59904059	HCPEpiC	choroid plexus:	n/a
49	chr15:59903968-59904018	LNCaP	prostate:	n/a
50	chr15:59904009-59904059	SK-N-SH_RA	brain:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:59885738..59888481-chr15:59900504..59902552,2	MCF-7	breast:
2	chr15:59900247..59901916-chr15:59903726..59905241,2	K562	blood:
3	chr15:59891038..59893878-chr15:59903015..59906504,3	K562	blood:

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCNT3-2	chr15:59901934-59902067	NONHSAT044179
2	lnc-GCNT3-2	chr15:59901934-59902067	NONHSAT044180
3	lnc-GCNT3-2	chr15:59901934-59902067	NONHSAT044181
4	lnc-GCNT3-2	chr15:59903591-59903875	NONHSAT044181
5	lnc-GCNT3-2	chr15:59901934-59902067	NONHSAT044178
6	lnc-GCNT3-2	chr15:59904101-59904180	NONHSAT044179
7	lnc-GCNT3-2	chr15:59904101-59904180	NONHSAT044178
8	lnc-GCNT3-2	chr15:59904101-59904180	NONHSAT044180

No data

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

Extended variants
information (count: 512 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:512 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs556986964	chr15:59898166-59898167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs547474869	chr15:59898212-59898213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs575340636	chr15:59898222-59898223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs542923733	chr15:59898238-59898239	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs115071294	chr15:59898248-59898249	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs74517877	chr15:59898250-59898251	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs540904915	chr15:59898261-59898262	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs149962508	chr15:59898264-59898265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs532706686	chr15:59898265-59898266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs551207783	chr15:59898273-59898274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs554735942	chr15:59898306-59898307	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs9920464	chr15:59898307-59898308	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs534327702	chr15:59898327-59898328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs530620560	chr15:59898330-59898331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs9920470	chr15:59898369-59898370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs144974997	chr15:59898378-59898379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs534339977	chr15:59898383-59898384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs546842595	chr15:59898391-59898392	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs189417239	chr15:59898396-59898397	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs538404370	chr15:59898460-59898461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs553968528	chr15:59898468-59898469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs11857723	chr15:59898487-59898488	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs536324035	chr15:59898522-59898523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs11857791	chr15:59898526-59898527	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs71425870	chr15:59898553-59898554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs573156483	chr15:59898556-59898557	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs71480537	chr15:59898567-59898568	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs71480538	chr15:59898569-59898570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs71480539	chr15:59898572-59898573	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs370802623	chr15:59898617-59898618	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs375023061	chr15:59898627-59898628	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs142189005	chr15:59898628-59898629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs182584846	chr15:59898642-59898643	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs577604998	chr15:59898645-59898646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs368103749	chr15:59898646-59898647	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs544968355	chr15:59898647-59898648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs146815243	chr15:59898648-59898649	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs112042916	chr15:59898669-59898670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs79098862	chr15:59898670-59898671	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs71119493	chr15:59898676-59898677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs147784675	chr15:59898677-59898678	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs71293995	chr15:59898678-59898679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs398070678	chr15:59898698-59898699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs184218713	chr15:59898699-59898700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs530354029	chr15:59898722-59898723	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs28517610	chr15:59898723-59898724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs374949407	chr15:59898724-59898725	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs367645539	chr15:59898729-59898730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs560843895	chr15:59898746-59898747	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs189328642	chr15:59898788-59898789	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

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
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59896600-59902000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr15:59896800-59911800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:59897400-59903400	Weak transcription	HepG2	liver
4	chr15:59897600-59901800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:59901800-59902200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr15:59902000-59902200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:59902000-59902200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:59902000-59902200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:59902000-59902200	Enhancers	Gastric	stomach
10	chr15:59902000-59902200	Enhancers	Pancreas	Pancrea
11	chr15:59902000-59902200	Enhancers	Stomach Mucosa	stomach
12	chr15:59902000-59902200	Enhancers	Spleen	Spleen
13	chr15:59902000-59902400	Enhancers	Duodenum Mucosa	Duodenum
14	chr15:59902000-59902400	ZNF genes & repeats	A549	lung
15	chr15:59902200-59903400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:59902200-59903600	Weak transcription	Pancreas	Pancrea
17	chr15:59902200-59903600	Weak transcription	Stomach Mucosa	stomach
18	chr15:59902200-59905000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr15:59902400-59903400	Weak transcription	A549	lung
20	chr15:59902400-59903600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:59902800-59904200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:59903000-59903200	Active TSS	HSMM	muscle
23	chr15:59903200-59903600	Flanking Active TSS	HSMM	muscle
24	chr15:59903400-59903600	Enhancers	Fetal Intestine Small	intestine
25	chr15:59903400-59903600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr15:59903400-59903600	Enhancers	Hela-S3	cervix
27	chr15:59903400-59903600	Enhancers	HepG2	liver
28	chr15:59903400-59903800	Flanking Active TSS	A549	lung
29	chr15:59903400-59905600	Enhancers	Fetal Intestine Large	intestine
30	chr15:59903600-59903800	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr15:59903600-59903800	Enhancers	Colonic Mucosa	Colon
32	chr15:59903600-59903800	Flanking Active TSS	Fetal Intestine Small	intestine
33	chr15:59903600-59903800	Flanking Active TSS	NHDF-Ad	bronchial
34	chr15:59903600-59904000	Enhancers	Liver	Liver
35	chr15:59903600-59904000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr15:59903600-59904200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:59903600-59904200	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr15:59903600-59904400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
39	chr15:59903600-59904400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:59903600-59904400	Enhancers	Pancreas	Pancrea
41	chr15:59903600-59904400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr15:59903600-59904400	Flanking Active TSS	Hela-S3	cervix
43	chr15:59903600-59905000	Active TSS	Rectal Smooth Muscle	rectum
44	chr15:59903600-59905200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr15:59903600-59905200	Flanking Active TSS	HepG2	liver
46	chr15:59903600-59905400	Active TSS	Stomach Mucosa	stomach
47	chr15:59903600-59907200	Active TSS	Duodenum Mucosa	Duodenum
48	chr15:59903800-59904000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr15:59903800-59904000	Weak transcription	Fetal Intestine Small	intestine
50	chr15:59903800-59904200	Weak transcription	Colonic Mucosa	Colon

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