Variant report

Variant	nsv542390
Chromosome Location	chr15:54951691-55266222
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55098177..55100063-chr15:55487437..55488979,2	MCF-7	breast:
2	chr15:55095085..55095585-chr3:11761302..11762189,2	MCF-7	breast:
3	chr15:55188424..55190542-chr15:55196033..55198017,2	K562	blood:
4	chr15:55062888..55065533-chr15:55066470..55069394,2	K562	blood:
5	chr15:55062888..55065533-chr15:55066470..55069394,2	K562	blood:
6	chr15:55108183..55110175-chr15:55112199..55114608,2	K562	blood:
7	chr15:55150804..55152762-chr15:55153752..55155795,2	K562	blood:
8	chr15:55000280..55003286-chr15:55005591..55008128,3	K562	blood:
9	chr15:55000191..55003653-chr15:55007581..55011163,3	MCF-7	breast:
10	chr15:55202578..55205059-chr15:55214627..55217518,2	K562	blood:
11	chr15:55102625..55104319-chr15:55107510..55110116,2	K562	blood:
12	chr15:55000280..55003286-chr15:55005591..55008128,3	K562	blood:
13	chr15:55189915..55191896-chr15:55191995..55194330,2	K562	blood:
14	chr15:55202578..55205059-chr15:55214627..55217518,2	K562	blood:
15	chr15:55188424..55190542-chr15:55196033..55198017,2	K562	blood:
16	chr15:55150804..55152762-chr15:55153752..55155795,2	K562	blood:
17	chr15:55108183..55110175-chr15:55112199..55114608,2	K562	blood:
18	chr15:55000191..55003653-chr15:55007581..55011163,3	MCF-7	breast:
19	chr15:55189915..55191896-chr15:55191995..55194330,2	K562	blood:
20	chr15:55102625..55104319-chr15:55107510..55110116,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UNC13C-3	chr15:55212817-55213114	ucExp_388_+
2	lnc-RSL24D1-3	chr15:55212817-55213114	ucExp_388_-

No data

Variant related genes	Relation type
ENSG00000137876	chromatin interactions
ENSG00000144560	chromatin interactions

Extended variants
information (count: 5469 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:5469 , 50 per page) page: 1 2 3 4 5 6 7 ... 110

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs140224270	chr15:54951724-54951725	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs185115142	chr15:54951725-54951726	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs60998616	chr15:54951769-54951770	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs552540317	chr15:54951783-54951784	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs566356617	chr15:54951815-54951816	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs535377145	chr15:54951824-54951825	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs145189964	chr15:54951834-54951835	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs568439754	chr15:54951859-54951860	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs76934752	chr15:54951864-54951865	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs536504348	chr15:54951878-54951879	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs573907536	chr15:54951932-54951933	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs577308729	chr15:54951936-54951937	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs16975039	chr15:54951937-54951938	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs184239260	chr15:54951943-54951944	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs28439305	chr15:54951948-54951949	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs540899346	chr15:54951995-54951996	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs560851699	chr15:54952014-54952015	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs574331383	chr15:54952016-54952017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs543088429	chr15:54952032-54952033	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs563392124	chr15:54952036-54952037	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs372512354	chr15:54952057-54952058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs139011198	chr15:54952061-54952062	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs546365091	chr15:54952069-54952070	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs754939	chr15:54952077-54952078	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs541658063	chr15:54952100-54952101	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs140696846	chr15:54952122-54952123	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs143664229	chr15:54952147-54952148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs569877563	chr15:54952225-54952226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs548856397	chr15:54952231-54952232	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs568780554	chr15:54952264-54952265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs10531840	chr15:54952278-54952279	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs369687412	chr15:54952281-54952282	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs530926148	chr15:54952340-54952341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs143774621	chr15:54952342-54952343	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs527407574	chr15:54952352-54952353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs148130282	chr15:54952373-54952374	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs188348745	chr15:54952401-54952402	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs534698609	chr15:54952416-54952417	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs553072055	chr15:54952449-54952450	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs565490142	chr15:54952502-54952503	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs193190470	chr15:54952528-54952529	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs74016823	chr15:54952564-54952565	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs75987173	chr15:54952568-54952569	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs543382125	chr15:54952573-54952574	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs182907651	chr15:54952575-54952576	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs141908532	chr15:54952586-54952587	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs545889027	chr15:54952615-54952616	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs559497248	chr15:54952673-54952674	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs16975041	chr15:54952699-54952700	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs150635181	chr15:54952705-54952706	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:70)

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
Renal cell carcinoma	21215367	CNVD
Cancer	20164919	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	21215367	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:190 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54951400-54952000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr15:54952000-54952400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:54952400-54952800	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr15:54968000-54968400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:54968600-54973200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:54970600-54970800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:54972400-54974600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:54972400-54975600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:54972600-54974600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:54973200-54973600	Enhancers	Primary hematopoietic stem cells	blood
11	chr15:54973600-54974400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr15:54973800-54974600	Enhancers	Primary B cells from cord blood	blood
13	chr15:54974400-54975800	Enhancers	Primary hematopoietic stem cells	blood
14	chr15:54974600-54975000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:54975000-54975600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr15:54979200-54979600	Enhancers	Pancreas	Pancrea
17	chr15:54979600-54980000	Active TSS	Pancreas	Pancrea
18	chr15:54979600-54980200	Enhancers	Liver	Liver
19	chr15:54979600-54980400	Active TSS	Duodenum Mucosa	Duodenum
20	chr15:54979600-54980400	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr15:54979600-54980400	Active TSS	A549	lung
22	chr15:54979600-54980600	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr15:54979800-54980400	Active TSS	Stomach Mucosa	stomach
24	chr15:54980000-54980400	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr15:54980000-54980600	Enhancers	Pancreas	Pancrea
26	chr15:54980400-54980600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr15:54980400-54980600	Enhancers	Stomach Mucosa	stomach
28	chr15:54982800-54983400	Enhancers	Brain Germinal Matrix	brain
29	chr15:55000200-55000800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:55019000-55020000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:55019200-55019400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:55019400-55019800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:55020000-55020400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:55020400-55021000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:55021000-55022200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:55022200-55023000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:55030400-55031000	ZNF genes & repeats	Adipose Nuclei	Adipose
38	chr15:55030400-55031000	ZNF genes & repeats	Aorta	Aorta
39	chr15:55037600-55037800	Weak transcription	Aorta	Aorta
40	chr15:55037800-55038200	ZNF genes & repeats	Aorta	Aorta
41	chr15:55038200-55041600	Weak transcription	Aorta	Aorta
42	chr15:55041800-55042000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:55055800-55056200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:55056200-55057200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:55057200-55057800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr15:55057800-55058000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:55062000-55062800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:55062000-55062800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr15:55062200-55062600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr15:55062200-55062800	Enhancers	HUES64 Cell Line	embryonic stem cell

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