Variant report

Variant	nsv984040
Chromosome Location	chr15:30337851-30338551
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:30338160-30338310	HRE	kidney:	n/a	n/a
2	CTCF	chr15:30338120-30338270	RPTEC	kidney:	n/a	n/a
3	CTCF	chr15:30338100-30338250	HCPEpiC	choroid plexus:	n/a	n/a
4	CTCF	chr15:30338134-30338199	Kidney_OC	kidney:	n/a	n/a
5	CTCF	chr15:30338088-30338231	MCF-7	breast:	n/a	n/a
6	CTCF	chr15:30338200-30338350	RPTEC	kidney:	n/a	n/a
7	CTCF	chr15:30338000-30338150	RPTEC	kidney:	n/a	n/a
8	CTCF	chr15:30338119-30338188	NHEK	skin:	n/a	n/a
9	CTCF	chr15:30338126-30338216	MCF-7	breast:	n/a	n/a
10	CTCF	chr15:30338100-30338250	NHEK	skin:	n/a	n/a
11	CTCF	chr15:30337960-30338110	HRE	kidney:	n/a	n/a
12	CTCF	chr15:30338071-30338223	MCF-7	breast:	n/a	n/a
13	EBF1	chr15:30337979-30338184	GM12878	blood:	n/a	n/a
14	EP300	chr15:30338400-30339252	SK-N-SH	brain:	n/a	n/a
15	FOXA1	chr15:30338015-30338227	T-47D	breast:	n/a	n/a
16	GTF2F1	chr15:30338212-30338229	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr15:30338402-30339220	SK-N-SH	brain:	n/a	n/a
18	MYC	chr15:30337997-30338055	MCF-7	breast:	n/a	n/a
19	POLR2A	chr15:30337897-30338044	A549	lung:	n/a	n/a
20	POLR2A	chr15:30337591-30338038	HepG2	liver:	n/a	n/a
21	POLR2A	chr15:30337100-30338242	GM12892	blood:	n/a	n/a
22	POLR2A	chr15:30337864-30338089	A549	lung:	n/a	n/a
23	POLR2A	chr15:30337872-30337992	GM12891	blood:	n/a	n/a
24	POLR2A	chr15:30337858-30338053	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr15:30337830-30338124	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:30337808-30338002	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:30337927-30338027	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr15:30337914-30338053	MCF-7	breast:	n/a	n/a
29	POLR2A	chr15:30337871-30338038	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:30337807-30338103	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:30336966-30338214	K562	blood:	n/a	n/a
32	POLR2A	chr15:30337772-30338136	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr15:30336793-30338244	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:30337711-30338122	A549	lung:	n/a	n/a
35	POLR2A	chr15:30337913-30338059	MCF-7	breast:	n/a	n/a
36	POLR2A	chr15:30337870-30337904	MCF-7	breast:	n/a	n/a
37	POLR2A	chr15:30337316-30338112	GM12891	blood:	n/a	n/a
38	POLR2A	chr15:30337230-30338284	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr15:30337139-30338184	MCF-7	breast:	n/a	n/a
40	POLR2A	chr15:30337855-30338053	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr15:30338051-30338069	Gliobla	brain:	n/a	n/a
42	POLR2A	chr15:30337981-30338232	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr15:30337991-30338146	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr15:30338014-30338244	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr15:30337950-30338403	ECC-1	luminal epithelium:	n/a	n/a
46	RAD21	chr15:30337931-30338336	H1-hESC	embryonic stem cell:	n/a	n/a
47	SPI1	chr15:30337926-30338135	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:30337875-30337925	MCF10A-Er-Src	breast:	n/a
2	chr15:30337875-30337925	HCF	heart:	n/a
3	chr15:30337875-30337925	HUVEC	blood vessel:	n/a
4	chr15:30337875-30337925	BJ	skin:	n/a
5	chr15:30337875-30337925	HEK293	kidney:	embryo
6	chr15:30337875-30337925	Hepatocyte	liver:	n/a
7	chr15:30337875-30337925	Hela-S3	cervix:	n/a
8	chr15:30337875-30337925	HEEpiC	esophagus:	n/a
9	chr15:30337875-30337925	A549	lung:	n/a
10	chr15:30337875-30337925	AG04449	skin:	fetal
11	chr15:30337875-30337925	AG09319	gingival:	n/a
12	chr15:30337875-30337925	SAEC	small airway:	n/a
13	chr15:30337875-30337925	LNCaP	prostate:	n/a
14	chr15:30337875-30337925	AG10803	skin:	n/a
15	chr15:30337875-30337925	HPAEpiC	pulmonary alveolar:	n/a
16	chr15:30337875-30337925	HRE	kidney:	n/a
17	chr15:30337875-30337925	SK-N-SH	brain:	n/a
18	chr15:30337875-30337925	T-47D	breast:	n/a
19	chr15:30337875-30337925	NHDF-neo	bronchial:	n/a
20	chr15:30337875-30337925	MCF-7	breast:	n/a
21	chr15:30337875-30337925	NB4	blood:	n/a
22	chr15:30337875-30337925	AG04450	lung:	fetal
23	chr15:30337875-30337925	SK-N-MC	brain:	n/a
24	chr15:30337875-30337925	HMEC	breast:	n/a
25	chr15:30337875-30337925	NH-A	brain:	n/a
26	chr15:30337875-30337925	ProgFib	skin:	n/a
27	chr15:30337875-30337925	HCPEpiC	choroid plexus:	n/a
28	chr15:30337875-30337925	HepG2	liver:	n/a
29	chr15:30337875-30337925	U87	brain:	n/a
30	chr15:30337875-30337925	K562	blood:	n/a
31	chr15:30337875-30337925	AoSMC	blood vessel:	n/a
32	chr15:30337875-30337925	Jurkat	blood:	n/a
33	chr15:30337875-30337925	Caco-2	colon:	n/a
34	chr15:30337875-30337925	GM12878	blood:	n/a
35	chr15:30337875-30337925	HRCEpiC	kidney:	n/a
36	chr15:30337875-30337925	PANC-1	pancreas:	n/a
37	chr15:30337875-30337925	NHBE	bronchial:	n/a
38	chr15:30337875-30337925	ovcar-3	ovarian:	n/a
39	chr15:30337875-30337925	H1-hESC	embryonic stem cell:	embryo
40	chr15:30337875-30337925	PrEC	prostate:	n/a
41	chr15:30337875-30337925	HIPEpiC	eye:	n/a
42	chr15:30337875-30337925	GM12891	blood:	n/a
43	chr15:30337875-30337925	IMR90	lung:	fetal
44	chr15:30337875-30337925	HRPEpiC	eye:	n/a
45	chr15:30337875-30337925	PFSK-1	brain:	n/a
46	chr15:30337875-30337925	ECC-1	luminal epithelium:	n/a
47	chr15:30337875-30337925	GM06990	blood:	n/a
48	chr15:30337875-30337925	SK-N-SH_RA	brain:	n/a
49	chr15:30337875-30337925	SKMC	muscle:	n/a
50	chr15:30337875-30337925	AG09309	skin:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TJP1-1	chr15:30337914-30338051	ENSG00000259647.1

No data

Variant related genes	Relation type
ENSG00000259647	TF binding region
ENSG00000259647	CpG island

Extended variants
information (count: 34 )
Associated
traits (count: 143 )

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs539494324	chr15:30337861-30337862	Enhancers Bivalent/Poised TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs552773978	chr15:30337876-30337877	Enhancers Bivalent/Poised TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs572832748	chr15:30337897-30337898	Enhancers Bivalent/Poised TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs143042433	chr15:30337907-30337908	Enhancers Bivalent/Poised TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs182207717	chr15:30337928-30337929	Enhancers Bivalent/Poised TSS Weak transcription Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
6	rs57819178	chr15:30337957-30337958	Enhancers Bivalent/Poised TSS Weak transcription Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs8040758	chr15:30338068-30338069	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs544428255	chr15:30338119-30338120	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs368141360	chr15:30338126-30338127	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs34294609	chr15:30338136-30338137	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs386782597	chr15:30338191-30338192	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs185992828	chr15:30338193-30338194	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs546312064	chr15:30338196-30338197	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs559581910	chr15:30338206-30338207	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs528510607	chr15:30338217-30338218	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs190994484	chr15:30338229-30338230	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs555588165	chr15:30338237-30338238	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs531078286	chr15:30338238-30338239	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs202122775	chr15:30338282-30338283	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs35876784	chr15:30338283-30338284	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs549701380	chr15:30338297-30338298	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs140239227	chr15:30338336-30338337	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs571054808	chr15:30338356-30338357	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs539631657	chr15:30338362-30338363	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs376309796	chr15:30338378-30338379	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs182842974	chr15:30338380-30338381	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs187087784	chr15:30338412-30338413	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs575738477	chr15:30338467-30338468	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs34037192	chr15:30338473-30338474	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs111945765	chr15:30338488-30338489	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs555361413	chr15:30338498-30338499	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs575630907	chr15:30338503-30338504	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs544544735	chr15:30338548-30338549	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs58954662	chr15:30338550-30338551	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:143)

Disease	PMID	Source
Ovarian cancer	21720365	CNVD
HDAC8	0	CNVD
NIPBL	0	CNVD
RAD21	0	CNVD
SMC1A	0	CNVD
SMC3	0	CNVD
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Prader-willi syndrome	21504564	CNVD
The inv dup or idic syndrome	19019226	CNVD
Prader-willi syndrome	21233802	CNVD
Angelman syndrome	16617304	CNVD
Angelman syndrome	20970697	CNVD
Autism	22958593	CNVD
Prader-willi syndrome	16617304	CNVD
Prader-willi syndrome	18923514	CNVD
Prader-willi syndrome	20970697	CNVD
Angelman syndrome	16183798	CNVD
Angelman syndrome	18923514	CNVD
Prader-willi syndrome	22241247	CNVD
Epilepsy	20970697	CNVD
Autism	20970697	CNVD
Autism	19935738	CNVD
Autism	22930557	CNVD
Autism	19966786	CNVD
Autism	18923514	CNVD
Autism	18925931	CNVD
Autism	18835857	CNVD
Prader-willi syndrome	18835857	CNVD
Prader-willi syndrome	22152151	CNVD
Autism	22241247	CNVD
15q-syndrome	21725066	CNVD
Prader-willi syndrome	21503198	CNVD
Autism	21956041	CNVD
Prader-willi syndrome	16760730	CNVD
Prader-willi syndrome	22470819	CNVD
prenatal diagnosis	20453657	CNVD
Prader-willi syndrome	17867985	CNVD
Angelman syndrome	21072004	CNVD
Acute lymphoblastic leukemia	20067559	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
Hodgkin''s lymphoma	18641027	CNVD
Prader-willi syndrome	18781185	CNVD
Melanoma	18172304	CNVD
Autism	17322880	CNVD
Prader-willi syndrome	19329560	CNVD
Autism	17999366	CNVD
Autism	17901113	CNVD
Neurodevelopmental disorder	17015230	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Mental retardation	18923513	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
Gastrointestinal stromal cancer	20818650	CNVD
Intellectual disability	22102821	CNVD
Hodgkin''s lymphoma	17606441	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	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
Breast cancer	21858162	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Angelman syndrome	18787571	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Abnormal corpus callosum	21572526	CNVD
idiopathic generalized epilepsy	19843651	CNVD
Autism	20531469	CNVD
Neuropsychiatric disorder	20506139	CNVD
Austim spectrum disorder	21302340	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Autism	19204725	CNVD
Schizophrenia	19204725	CNVD
Schizophrenia	19149910	CNVD
Schizophrenia	20967226	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Autism	22543975	CNVD
Epilepsy	22499536	CNVD
Schizophrenia	22499536	CNVD
Schizophrenia	18923514	CNVD
Bipolar disorder	19114987	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20553308	CNVD
Schizophrenia	21956041	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Mental retardation	21956041	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Autism	21269290	CNVD
Intellectual disability	21269290	CNVD
Schizophrenia	21269290	CNVD
Colorectal cancer	21128281	CNVD
Epilepsy	19289393	CNVD
Epilepsy	20643615	CNVD
Mental retardation	19289393	CNVD
Mental retardation	20152051	CNVD
Schizophrenia	19289393	CNVD
dysmorphic features	19289393	CNVD
idiopathic epilepsies	19341504	CNVD
idiopathic generalized epilepsy	19592580	CNVD
idiopathic generalized epilepsy	19136953	CNVD
Autism	22094647	CNVD
Developmental delay	19898479	CNVD
Mental retardation	18278044	CNVD
Mental retardation	19898479	CNVD
Prader-willi syndrome	18854863	CNVD
Schizophrenia	19855392	CNVD
Ovarian cancer	22174824	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Cancer	20164919	CNVD

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30335400-30338600	Weak transcription	HSMM	muscle
2	chr15:30335600-30338000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:30335600-30338600	Weak transcription	Fetal Kidney	kidney
4	chr15:30335600-30338800	Weak transcription	A549	lung
5	chr15:30335600-30341200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr15:30335600-30342400	Weak transcription	Liver	Liver
7	chr15:30335800-30338000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:30336800-30338000	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr15:30337000-30338200	Active TSS	Colonic Mucosa	Colon
10	chr15:30337200-30338200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:30337400-30338200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:30337600-30338000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:30337600-30338200	Active TSS	Duodenum Mucosa	Duodenum
14	chr15:30337600-30338200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr15:30337800-30338000	Enhancers	Brain Substantia Nigra	brain
16	chr15:30337800-30338200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr15:30337800-30338400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr15:30337800-30338800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr15:30337800-30339000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:30338000-30338200	Enhancers	Brain Cingulate Gyrus	brain
21	chr15:30338000-30338600	Weak transcription	Brain Substantia Nigra	brain
22	chr15:30338000-30338800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr15:30338000-30338800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:30338000-30339000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr15:30338200-30338800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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