Variant report

Variant	nsv932912
Chromosome Location	chr17:19555923-19556219
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	CEBPB	chr17:19555988-19556295	HepG2	liver:	n/a	n/a
2	CEBPB	chr17:19556033-19556201	HepG2	liver:	n/a	n/a
3	CEBPB	chr17:19555990-19556286	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr17:19555969-19556309	A549	lung:	n/a	n/a
5	EP300	chr17:19555870-19556265	T-47D	breast:	n/a	chr17:19555978-19555988
6	FOS	chr17:19555168-19556317	MCF10A-Er-Src	breast:	n/a	chr17:19555328-19555340 chr17:19555330-19555338 chr17:19555329-19555339
7	FOS	chr17:19555045-19556263	MCF10A-Er-Src	breast:	n/a	chr17:19555328-19555340 chr17:19555330-19555338 chr17:19555329-19555339
8	FOS	chr17:19555169-19556316	MCF10A-Er-Src	breast:	n/a	chr17:19555328-19555340 chr17:19555330-19555338 chr17:19555329-19555339
9	FOS	chr17:19555923-19556300	MCF10A-Er-Src	breast:	n/a	n/a
10	FOXA1	chr17:19555766-19556229	T-47D	breast:	n/a	n/a
11	FOXA1	chr17:19555883-19556251	T-47D	breast:	n/a	n/a
12	GATA3	chr17:19555925-19556321	T-47D	breast:	n/a	n/a
13	MYC	chr17:19554917-19556211	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr17:19555877-19556226	MCF10A-Er-Src	breast:	n/a	n/a
15	NFIC	chr17:19556049-19556306	HepG2	liver:	n/a	chr17:19556165-19556181 chr17:19556164-19556181
16	POLR2A	chr17:19555841-19556175	MCF10A-Er-Src	breast:	n/a	n/a
17	STAT3	chr17:19555936-19556183	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr17:19555912-19556206	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19553955..19556054-chr17:19560448..19564216,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264932	TF binding region
ALDH3A2	TF binding region
ENSG00000072210	chromatin interactions

Extended variants
information (count: 15 )
Associated
traits (count: 153 )

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs149865400	chr17:19555939-19555940	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs370250271	chr17:19555963-19555964	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs370969679	chr17:19555971-19555972	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs563546027	chr17:19555973-19555974	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs1004491	chr17:19555976-19555977	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs377025343	chr17:19555978-19555979	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs552272011	chr17:19556020-19556021	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs559616929	chr17:19556035-19556036	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs575574317	chr17:19556047-19556048	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs528468655	chr17:19556063-19556064	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region	2 gene(s)	Overlapped CNVs	n/a
11	rs548332530	chr17:19556067-19556068	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region	2 gene(s)	Overlapped CNVs	n/a
12	rs568339339	chr17:19556092-19556093	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region	2 gene(s)	Overlapped CNVs	n/a
13	rs202105328	chr17:19556187-19556188	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region	2 gene(s)	Overlapped CNVs	n/a
14	rs34368630	chr17:19556188-19556189	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region	2 gene(s)	Overlapped CNVs	n/a
15	rs375572489	chr17:19556191-19556192	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:153)

Disease	PMID	Source
Burkitt''s lymphoma	19759907	CNVD
Wilms tumour	21544195	CNVD
Esophageal adenocarcinoma	18519675	CNVD
lymphocytic leukemia	21291569	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Melanoma	18172304	CNVD
Medulloblastoma	21979893	CNVD
Breast cancer	16608533	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Chordoma	21602918	CNVD
Miller-Dieker syndrome	22283845	CNVD
Non-syndromic sensorineural hearing loss	17457615	CNVD
Cancer	22429812	CNVD
Chronic lymphocytic leukemia	21795749	CNVD
Ewing''s sarcoma	21437220	CNVD
Follicular lymphoma	19010834	CNVD
Colorectal cancer	20709793	CNVD
Acute myeloid leukemia	16864856	CNVD
Endometrial cancer	22040021	CNVD
Paraganglioma	21461997	CNVD
Pheochromocytoma	21461997	CNVD
Breast cancer	22028636	CNVD
Breast cancer	20837533	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
colon cancer	17210682	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Basal cell lymphoma	17053054	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Colorectal cancer	19359472	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Chronic lymphocytic leukemia	17971485	CNVD
Basal cell lymphoma	17170743	CNVD
Breast cancer	16461572	CNVD
Colorectal cancer	16272173	CNVD
Follicular lymphoma	17170743	CNVD
Human rectal carcinomas	16397240	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	17133270	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Ovarian cancer	22174824	CNVD
Moyamoya disease	22323933	CNVD
small cell lung cancer	20016488	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute promyelocytic leukemia	19109227	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	21251322	CNVD
Myelodysplastic syndrome	21251322	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Acute myeloid leukemia	20724749	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Acute myeloid leukemia	17237825	CNVD
Colorectal cancer	21645411	CNVD
HIV/AIDS	22844521	CNVD
Psoriasis	22844521	CNVD
Rheumatoid arthritis	22844521	CNVD
Sclerosis systemic	22844521	CNVD
Systemic lupus erythematosus	22844521	CNVD
HIV/AIDS	17953491	CNVD
HIV/AIDS	20877625	CNVD
Immune disease	21076436	CNVD
Rheumatoid arthritis	17953491	CNVD
Type 1 diabetes	17953491	CNVD
HIV/AIDS	15637236	CNVD
Prostate cancer	18632612	CNVD
Lung cancer	18438408	CNVD
Ovarian cancer	21781307	CNVD
Autism	22495311	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Neurofibromatosis	18196300	CNVD
Colorectal cancer	16774939	CNVD
Breast cancer	17001317	CNVD
Rhabdomyosarcoma	16790082	CNVD
Charcot-marie-tooth disease	16463004	CNVD
Osteosarcoma	22292074	CNVD
Breast cancer	17603634	CNVD
Charcot	16760730	CNVD
Mental retardation	17901693	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
ovarian endometriomas	16273235	CNVD
Smith-Magenis syndrome	18923513	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16272173	CNVD
Austim spectrum disorder	21302340	CNVD
Autism	22492990	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	18414209	CNVD
Developmental delay	21549014	CNVD
Epilepsy	20970697	CNVD
Mental retardation	18414209	CNVD
Mental retardation	21549014	CNVD
Smith-Magenis syndrome	21981782	CNVD
Smith-Magenis syndrome	20188345	CNVD
Smith-Magenis syndrome	16775514	CNVD
Smith-Magenis syndrome	22585170	CNVD
Smith-Magenis syndrome	22241247	CNVD
Autism	20970697	CNVD
Mental retardation	19951919	CNVD
Potocki-Lupski syndrome	21271655	CNVD
Potocki-lupski syndrome	17357070	CNVD
Potocki-lupski syndrome	20110824	CNVD
Potocki-lupski syndrome	18923514	CNVD
Potocki-lupski syndrome	22241247	CNVD
Potocki-lupski syndrome	20188345	CNVD
Schizophrenia	21399695	CNVD
Mental retardation	16773131	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Non-small cell lung cancer	21829676	CNVD
Glioblastoma multiforme	17002787	CNVD
Charcot-marie-tooth disease	22470819	CNVD
Neurofibromatosis	22470819	CNVD
Neuropathy	22470819	CNVD
Smith-Magenis syndrome	18301319	CNVD
Smith-Magenis syndrome	17357070	CNVD
Smith-Magenis syndrome	18469339	CNVD
Smith-Magenis syndrome	22241097	CNVD
Smith-Magenis syndrome	22470819	CNVD
Tourette syndrome	18923514	CNVD
Type 1 diabetes	22470819	CNVD
Potocki-lupski syndrome	18469339	CNVD
Follicular lymphoma	20505157	CNVD
T-cell lymphomas	19863542	CNVD
Neuropathy	17597781	CNVD
Hepatocellular carcinoma	16750200	CNVD
Neurodevelopmental disorder	17015230	CNVD
Smith-Magenis syndrome	17597781	CNVD
Potocki-lupski syndrome	18059269	CNVD
Potocki-lupski syndrome	17597781	CNVD
Mental retardation	17847001	CNVD
Multiple myeloma	16616336	CNVD
Breast cancer	20409316	CNVD
Autism	22543975	CNVD
Sezary syndrome	18413736	CNVD
Cancer	20164920	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:149 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19552600-19556400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:19552800-19557600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:19552800-19557800	Weak transcription	Placenta	Placenta
4	chr17:19553200-19556000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:19553200-19556000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr17:19553200-19556600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr17:19553200-19556800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:19553200-19557800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:19553200-19558200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:19553200-19558200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:19553200-19558400	Weak transcription	Primary T cells from cord blood	blood
12	chr17:19553200-19566800	Weak transcription	Primary B cells from cord blood	blood
13	chr17:19553200-19577400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr17:19553200-19580000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr17:19553400-19556000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:19553400-19556200	Enhancers	Fetal Lung	lung
17	chr17:19553400-19556400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr17:19553400-19556800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr17:19553400-19556800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:19553400-19558200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:19553400-19566400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr17:19553600-19556400	Enhancers	Osteobl	bone
23	chr17:19553600-19557600	Weak transcription	Ovary	ovary
24	chr17:19553800-19556000	Enhancers	Colon Smooth Muscle	Colon
25	chr17:19553800-19556000	Enhancers	Pancreas	Pancrea
26	chr17:19553800-19556000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr17:19553800-19556200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr17:19553800-19556600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr17:19553800-19556800	Weak transcription	Spleen	Spleen
30	chr17:19553800-19560000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr17:19554000-19556000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:19554000-19556200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:19554000-19556200	Transcr. at gene 5' and 3'	A549	lung
34	chr17:19554200-19556400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:19554400-19556400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr17:19554400-19559400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr17:19554600-19556200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr17:19554600-19556200	Enhancers	Fetal Intestine Small	intestine
39	chr17:19554600-19557000	Enhancers	Stomach Mucosa	stomach
40	chr17:19554800-19556600	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr17:19554800-19574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:19555000-19556000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:19555000-19556000	Enhancers	Fetal Kidney	kidney
44	chr17:19555000-19556400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr17:19555000-19556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:19555000-19556600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr17:19555000-19556600	Genic enhancers	Adipose Nuclei	Adipose
48	chr17:19555000-19558200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr17:19555000-19558200	Weak transcription	Fetal Brain Male	brain
50	chr17:19555000-19558400	Weak transcription	HSMM	muscle

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