Variant report

Variant	esv3452945
Chromosome Location	chr1:62115764-62120662
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:366)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:62119887-62119892	Fibrobl	skin:	n/a	n/a
2	CTCF	chr1:62119900-62119915	Fibrobl	skin:	n/a	n/a
3	CTCF	chr1:62118629-62118661	Spleen_OC	spleen:	n/a	n/a
4	FOXA1	chr1:62116322-62116620	T-47D	breast:	n/a	n/a
5	FOXA1	chr1:62116307-62116558	T-47D	breast:	n/a	n/a
6	GATA3	chr1:62116359-62116578	T-47D	breast:	n/a	n/a
7	GATA3	chr1:62116259-62116598	T-47D	breast:	n/a	n/a
8	POLR2A	chr1:62120359-62120371	MCF-7	breast:	n/a	n/a
9	POLR2A	chr1:62120402-62120505	MCF-7	breast:	n/a	n/a
10	POLR2A	chr1:62117975-62118015	ProgFib	skin:	n/a	n/a
11	RCOR1	chr1:62118152-62118191	K562	blood:	n/a	n/a

(count:366 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:62119829-62119879	NB4	blood:	n/a
2	chr1:62120090-62120140	SAEC	small airway:	n/a
3	chr1:62119764-62119814	Hepatocyte	liver:	n/a
4	chr1:62120002-62120052	NH-A	brain:	n/a
5	chr1:62120040-62120090	Jurkat	blood:	n/a
6	chr1:62119829-62119879	GM06990	blood:	n/a
7	chr1:62120090-62120140	PANC-1	pancreas:	n/a
8	chr1:62119764-62119814	NT2-D1	testis:	n/a
9	chr1:62119829-62119879	MCF-7	breast:	n/a
10	chr1:62119764-62119814	Jurkat	blood:	n/a
11	chr1:62120405-62120455	MCF-7	breast:	n/a
12	chr1:62120040-62120090	HIPEpiC	eye:	n/a
13	chr1:62120040-62120090	K562	blood:	n/a
14	chr1:62120040-62120090	HRPEpiC	eye:	n/a
15	chr1:62120002-62120052	IMR90	lung:	fetal
16	chr1:62120002-62120052	BJ	skin:	n/a
17	chr1:62120040-62120090	MCF10A-Er-Src	breast:	n/a
18	chr1:62120040-62120090	SKMC	muscle:	n/a
19	chr1:62120040-62120090	AG04450	lung:	fetal
20	chr1:62120002-62120052	T-47D	breast:	n/a
21	chr1:62119829-62119879	NHBE	bronchial:	n/a
22	chr1:62120002-62120052	HAEpiC	amniotic membrane:	n/a
23	chr1:62120405-62120455	U87	brain:	n/a
24	chr1:62119764-62119814	AG04450	lung:	fetal
25	chr1:62119829-62119879	GM12878	blood:	n/a
26	chr1:62120405-62120455	HCM	heart:	n/a
27	chr1:62120090-62120140	NH-A	brain:	n/a
28	chr1:62120002-62120052	MCF10A-Er-Src	breast:	n/a
29	chr1:62119829-62119879	AG09309	skin:	n/a
30	chr1:62120090-62120140	MCF-7	breast:	n/a
31	chr1:62120405-62120455	Caco-2	colon:	n/a
32	chr1:62120002-62120052	HEEpiC	esophagus:	n/a
33	chr1:62120405-62120455	SK-N-SH_RA	brain:	n/a
34	chr1:62120090-62120140	GM12891	blood:	n/a
35	chr1:62120090-62120140	GM12892	blood:	n/a
36	chr1:62119764-62119814	ProgFib	skin:	n/a
37	chr1:62120405-62120455	LNCaP	prostate:	n/a
38	chr1:62120090-62120140	CMK	blood:	n/a
39	chr1:62120405-62120455	HAEpiC	amniotic membrane:	n/a
40	chr1:62119829-62119879	SKMC	muscle:	n/a
41	chr1:62119829-62119879	Hepatocyte	liver:	n/a
42	chr1:62119764-62119814	HRE	kidney:	n/a
43	chr1:62120002-62120052	AG09319	gingival:	n/a
44	chr1:62120090-62120140	Jurkat	blood:	n/a
45	chr1:62120405-62120455	BE2_C	brain:	n/a
46	chr1:62120002-62120052	Caco-2	colon:	n/a
47	chr1:62120040-62120090	PFSK-1	brain:	n/a
48	chr1:62120405-62120455	BJ	skin:	n/a
49	chr1:62120090-62120140	GM12878	blood:	n/a
50	chr1:62120040-62120090	MCF-7	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62110139..62113045-chr1:62113882..62116057,2	K562	blood:
2	chr1:62106350..62108369-chr1:62114638..62116326,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INADL-4	chr1:62119914-62121800	NR_073400

No data

Variant related genes	Relation type
ENSG00000223920	TF binding region
ENSG00000223920	CpG island

Extended variants
information (count: 160 )
Associated
traits (count: 94 )

Variant overlapped rSNPs/rCNVs (count:160 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12048380	chr1:62115777-62115778	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs151025700	chr1:62115793-62115794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs553270959	chr1:62115816-62115817	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs114089655	chr1:62115840-62115841	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs114638423	chr1:62115843-62115844	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs185394151	chr1:62115855-62115856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs575194197	chr1:62115888-62115889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs140937316	chr1:62115889-62115890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs555538757	chr1:62115900-62115901	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs576648513	chr1:62115904-62115905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs12737794	chr1:62115941-62115942	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs138653569	chr1:62115945-62115946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs190206574	chr1:62115967-62115968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs530042201	chr1:62116039-62116040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs60396452	chr1:62116090-62116091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs548182676	chr1:62116117-62116118	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs34758984	chr1:62116132-62116133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs563272914	chr1:62116212-62116213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs530487749	chr1:62116259-62116260	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs12045540	chr1:62116288-62116289	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs182107091	chr1:62116384-62116385	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs72923653	chr1:62116391-62116392	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs534781996	chr1:62116479-62116480	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs562745062	chr1:62116546-62116547	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs533275343	chr1:62116549-62116550	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs545009786	chr1:62116587-62116588	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs547213231	chr1:62116638-62116639	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs141476453	chr1:62116695-62116696	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs6587938	chr1:62116806-62116807	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs557331582	chr1:62116808-62116809	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs146978101	chr1:62116813-62116814	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs535170058	chr1:62116852-62116853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs557708312	chr1:62116906-62116907	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs1353425	chr1:62116913-62116914	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs372780911	chr1:62116942-62116943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs528523739	chr1:62116959-62116960	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs559544743	chr1:62117016-62117017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs138157948	chr1:62117078-62117079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs116751199	chr1:62117156-62117157	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs563548695	chr1:62117157-62117158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs530806657	chr1:62117211-62117212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs552238137	chr1:62117233-62117234	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs372735611	chr1:62117244-62117245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs200927920	chr1:62117246-62117247	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs187922778	chr1:62117290-62117291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs191818914	chr1:62117299-62117300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs184060180	chr1:62117312-62117313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs188961162	chr1:62117313-62117314	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs78666464	chr1:62117336-62117337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs547062299	chr1:62117346-62117347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:94)

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
Medullary thyroid carcinoma	18765511	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Bipolar disorder	19114987	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62103400-62146400	Weak transcription	Gastric	stomach
2	chr1:62117800-62118200	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr1:62117800-62118400	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:62119600-62119800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:62119800-62120000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:62119800-62120400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:62120000-62121000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:62120400-62148200	Weak transcription	Aorta	Aorta

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