Variant report

Variant	nsv546379
Chromosome Location	chr1:62111054-62118178
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr1:62112891-62113154	HepG2	liver:	n/a	n/a
2	CEBPB	chr1:62113754-62113947	K562	blood:	n/a	n/a
3	CEBPB	chr1:62113772-62113972	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr1:62111272-62111424	MCF-7	breast:	n/a	n/a
5	CTCF	chr1:62111285-62111415	MCF-7	breast:	n/a	n/a
6	CTCF	chr1:62111264-62111437	MCF-7	breast:	n/a	n/a
7	CTCF	chr1:62111283-62111409	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:62111278-62111423	MCF-7	breast:	n/a	n/a
9	FOXA1	chr1:62112903-62113098	HepG2	liver:	n/a	chr1:62113019-62113034
10	FOXA1	chr1:62112873-62113092	HepG2	liver:	n/a	chr1:62113019-62113034
11	FOXA1	chr1:62111044-62111252	T-47D	breast:	n/a	n/a
12	FOXA1	chr1:62116322-62116620	T-47D	breast:	n/a	n/a
13	FOXA1	chr1:62116307-62116558	T-47D	breast:	n/a	n/a
14	FOXA1	chr1:62112832-62113155	HepG2	liver:	n/a	chr1:62113019-62113034
15	FOXA1	chr1:62112882-62113105	HepG2	liver:	n/a	chr1:62113019-62113034
16	FOXA2	chr1:62112881-62113100	HepG2	liver:	n/a	n/a
17	GATA3	chr1:62116259-62116598	T-47D	breast:	n/a	n/a
18	GATA3	chr1:62116359-62116578	T-47D	breast:	n/a	n/a
19	MYC	chr1:62111333-62111381	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:62117975-62118015	ProgFib	skin:	n/a	n/a
21	RCOR1	chr1:62118152-62118191	K562	blood:	n/a	n/a
22	SPI1	chr1:62114351-62114789	HL-60	blood:	n/a	n/a
23	UBTF	chr1:62114417-62114490	K562	blood:	n/a	n/a
24	ZKSCAN1	chr1:62113790-62114420	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:62110139..62113045-chr1:62113882..62116057,2	K562	blood:
2	chr1:62110139..62113045-chr1:62113882..62116057,2	K562	blood:
3	chr1:62107692..62111975-chr1:62207507..62210400,5	MCF-7	breast:
4	chr1:62106350..62108369-chr1:62114638..62116326,2	K562	blood:
5	chr1:62109498..62111908-chr1:62214585..62216451,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INADL-1	chr1:62113728-62113990	XLOC_000227

No data

Variant related genes	Relation type
ENSG00000223920	TF binding region
ENSG00000132849	chromatin interactions
ENSG00000271200	chromatin interactions

Extended variants
information (count: 221 )
Associated
traits (count: 94 )

Variant overlapped rSNPs/rCNVs (count:221 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2886326	chr1:62111054-62111055	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs12095123	chr1:62111089-62111090	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs550606510	chr1:62111117-62111118	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs552351267	chr1:62111145-62111146	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs567526329	chr1:62111146-62111147	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs182305829	chr1:62111157-62111158	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs550655950	chr1:62111163-62111164	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs187658047	chr1:62111167-62111168	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs570929841	chr1:62111196-62111197	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs35750449	chr1:62111243-62111244	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs371180874	chr1:62111262-62111263	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs145625633	chr1:62111322-62111323	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs553171694	chr1:62111323-62111324	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs138177434	chr1:62111456-62111457	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs566716922	chr1:62111460-62111461	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs528015735	chr1:62111527-62111528	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs549369687	chr1:62111557-62111558	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs567652808	chr1:62111574-62111575	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs149534065	chr1:62111604-62111605	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs556633550	chr1:62111616-62111617	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs571802515	chr1:62111619-62111620	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs371780188	chr1:62111658-62111659	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs143190290	chr1:62111666-62111667	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs193273796	chr1:62111692-62111693	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs11578823	chr1:62111694-62111695	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs555327326	chr1:62111761-62111762	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs115759104	chr1:62111765-62111766	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs543829863	chr1:62111794-62111795	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs562491576	chr1:62111797-62111798	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs532907356	chr1:62111807-62111808	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs544692164	chr1:62111868-62111869	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs148233983	chr1:62111878-62111879	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs142816054	chr1:62111906-62111907	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs201856226	chr1:62111933-62111934	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs549671028	chr1:62111951-62111952	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs545351982	chr1:62111952-62111953	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs567828524	chr1:62112060-62112061	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs532015802	chr1:62112109-62112110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs375940022	chr1:62112156-62112157	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs147369963	chr1:62112206-62112207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs571665746	chr1:62112215-62112216	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs1353424	chr1:62112229-62112230	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs139063027	chr1:62112241-62112242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs372758987	chr1:62112243-62112244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs185031927	chr1:62112279-62112280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs190274431	chr1:62112289-62112290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs139543188	chr1:62112483-62112484	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs557279074	chr1:62112487-62112488	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs574852070	chr1:62112527-62112528	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs555652590	chr1:62112553-62112554	Weak transcription Enhancers	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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62103400-62146400	Weak transcription	Gastric	stomach
2	chr1:62108000-62112800	Weak transcription	Ovary	ovary
3	chr1:62108600-62111200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:62108600-62112400	Weak transcription	Stomach Mucosa	stomach
5	chr1:62110200-62111200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:62111200-62111400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:62111400-62111600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:62112400-62113000	Enhancers	Stomach Mucosa	stomach
9	chr1:62112600-62113000	Enhancers	HepG2	liver
10	chr1:62112800-62113000	Enhancers	Ovary	ovary
11	chr1:62114400-62115000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:62117800-62118200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:62117800-62118400	Enhancers	Primary hematopoietic stem cells	blood

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