Variant report

Variant	esv3502173
Chromosome Location	chr1:63151769-63152216
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	GATA3	chr1:63150861-63151880	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr1:63150758-63151859	SK-N-SH	brain:	n/a	n/a
3	JUN	chr1:63151737-63152356	HepG2	liver:	n/a	chr1:63152175-63152188 chr1:63152176-63152185
4	JUND	chr1:63151730-63152358	HepG2	liver:	n/a	chr1:63152176-63152185
5	MXI1	chr1:63152116-63154856	SK-N-SH	brain:	n/a	n/a
6	RCOR1	chr1:63152200-63154891	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:63151590..63154458-chr1:63248689..63250715,2	K562	blood:
2	chr1:63141617..63143983-chr1:63151351..63153918,2	MCF-7	breast:
3	chr1:63146913..63149001-chr1:63152180..63153818,3	MCF-7	breast:
4	chr1:63144223..63146231-chr1:63150074..63152820,2	K562	blood:
5	chr1:63151590..63154458-chr1:63248689..63251365,3	K562	blood:

Variant related genes	Relation type
ENSG00000235545	TF binding region
ENSG00000125703	chromatin interactions

Extended variants
information (count: 11 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs201040350	chr1:63151790-63151791	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs116475209	chr1:63151802-63151803	Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs1185240	chr1:63151829-63151830	Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs373594458	chr1:63151836-63151837	Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs377019132	chr1:63151837-63151838	Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs371485710	chr1:63151839-63151840	Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs200884213	chr1:63152156-63152157	Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs77897785	chr1:63152158-63152159	Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs150751978	chr1:63152201-63152202	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs543061176	chr1:63152208-63152209	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs77346467	chr1:63152213-63152214	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Breast cancer	16620391	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
CNS Malformation Syndrome	17530927	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Colorectal cancer	20459617	CNVD
Endometrioid adenocarcinoma	16974079	CNVD

Chromatin state (count:155 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63112400-63152400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:63113600-63152800	Weak transcription	Primary B cells from cord blood	blood
3	chr1:63138000-63153000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:63141400-63152600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:63142800-63152400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:63143000-63152400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:63143000-63153000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:63147600-63152600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:63148200-63152600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:63148400-63152600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:63148600-63153000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:63148800-63152200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:63148800-63152800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:63148800-63152800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:63149000-63152800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:63149000-63152800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:63149600-63152600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:63150000-63153000	Enhancers	Liver	Liver
19	chr1:63150200-63151800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:63150200-63151800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:63150200-63152200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:63150200-63152400	Enhancers	A549	lung
23	chr1:63150200-63152800	Enhancers	Adipose Nuclei	Adipose
24	chr1:63150200-63152800	Enhancers	Fetal Brain Male	brain
25	chr1:63150200-63153000	Enhancers	Fetal Lung	lung
26	chr1:63150400-63152400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:63150600-63151800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:63150600-63152400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:63150600-63152400	Enhancers	NH-A	brain
30	chr1:63150600-63152800	Enhancers	Stomach Mucosa	stomach
31	chr1:63150800-63151800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:63150800-63151800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:63150800-63151800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:63150800-63151800	Enhancers	Ovary	ovary
35	chr1:63150800-63151800	Enhancers	Rectal Smooth Muscle	rectum
36	chr1:63150800-63151800	Genic enhancers	HSMM	muscle
37	chr1:63150800-63151800	Enhancers	HSMMtube	muscle
38	chr1:63150800-63152200	Enhancers	Osteobl	bone
39	chr1:63150800-63152600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:63150800-63152600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:63150800-63152600	Enhancers	Duodenum Mucosa	Duodenum
42	chr1:63150800-63152600	Enhancers	Fetal Intestine Small	intestine
43	chr1:63150800-63152600	Enhancers	HMEC	breast
44	chr1:63150800-63152800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr1:63150800-63152800	Enhancers	K562	blood
46	chr1:63150800-63153000	Enhancers	Fetal Heart	heart
47	chr1:63151000-63151800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:63151000-63151800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:63151000-63151800	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr1:63151000-63152000	Enhancers	Primary hematopoietic stem cells	blood

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