Variant report

Variant	nsv823854
Chromosome Location	chr6:140385359-140392243
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	chr6:140392168-140392714	MCF-7	breast:	n/a	n/a
2	CEBPB	chr6:140392234-140393394	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr6:140385600-140385750	HCPEpiC	choroid plexus:	n/a	n/a
4	CTCF	chr6:140385540-140385690	RPTEC	kidney:	n/a	n/a
5	CTCF	chr6:140385720-140385777	Kidney_OC	kidney:	n/a	n/a
6	CTCF	chr6:140385620-140385770	Caco-2	colon:	n/a	n/a
7	CTCF	chr6:140385660-140385810	HCPEpiC	choroid plexus:	n/a	n/a
8	CUX1	chr6:140385597-140385629	K562	blood:	n/a	n/a
9	EP300	chr6:140391912-140393685	SK-N-SH	brain:	n/a	chr6:140393627-140393636 chr6:140393626-140393640 chr6:140393598-140393608
10	EP300	chr6:140392197-140393535	SK-N-SH_RA	brain:	n/a	n/a
11	EP300	chr6:140392018-140393529	SK-N-SH	brain:	n/a	n/a
12	EP300	chr6:140392024-140393656	SK-N-SH	brain:	n/a	chr6:140393627-140393636 chr6:140393626-140393640 chr6:140393598-140393608
13	FOSL2	chr6:140392204-140393524	SK-N-SH	brain:	n/a	chr6:140393233-140393241
14	FOXM1	chr6:140392204-140393464	SK-N-SH	brain:	n/a	n/a
15	FOXM1	chr6:140391944-140393707	SK-N-SH	brain:	n/a	n/a
16	GATA2	chr6:140392181-140392687	SH-SY5Y	brain:	n/a	n/a
17	GATA3	chr6:140392013-140393312	MCF-7	breast:	n/a	chr6:140392062-140392073
18	GATA3	chr6:140391982-140393710	SK-N-SH	brain:	n/a	chr6:140392062-140392073 chr6:140393628-140393638
19	GATA3	chr6:140391703-140393691	SK-N-SH	brain:	n/a	chr6:140392062-140392073 chr6:140391881-140391891 chr6:140393628-140393638
20	GATA3	chr6:140391970-140393538	MCF-7	breast:	n/a	chr6:140392062-140392073
21	JUND	chr6:140392098-140393536	SK-N-SH	brain:	n/a	chr6:140393233-140393241
22	JUND	chr6:140392100-140393433	SK-N-SH	brain:	n/a	chr6:140393233-140393241
23	KAP1	chr6:140392223-140393107	U2OS	brain:	n/a	n/a
24	MEF2A	chr6:140392114-140393514	SK-N-SH	brain:	n/a	n/a
25	MEF2A	chr6:140392230-140393468	SK-N-SH	brain:	n/a	n/a
26	NFIC	chr6:140392130-140393335	SK-N-SH	brain:	n/a	chr6:140392443-140392460 chr6:140392444-140392460
27	NFIC	chr6:140391987-140393584	SK-N-SH	brain:	n/a	chr6:140392443-140392460 chr6:140392444-140392460
28	NR2F2	chr6:140392233-140392713	MCF-7	breast:	n/a	n/a
29	NR2F2	chr6:140392134-140392759	MCF-7	breast:	n/a	n/a
30	PBX3	chr6:140392072-140393631	SK-N-SH	brain:	n/a	n/a
31	PBX3	chr6:140392016-140393591	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr6:140392207-140392737	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr6:140386753-140386820	ProgFib	skin:	n/a	n/a
34	POLR2A	chr6:140392194-140392214	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr6:140392100-140392330	ProgFib	skin:	n/a	n/a
36	POLR2A	chr6:140392133-140393394	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr6:140390678-140390802	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr6:140391724-140391928	ProgFib	skin:	n/a	n/a
39	RAD21	chr6:140392193-140393348	Hela-S3	cervix:	n/a	n/a
40	RCOR1	chr6:140386550-140386558	GM12878	blood:	n/a	n/a
41	SIN3AK20	chr6:140392081-140393336	MCF-7	breast:	n/a	n/a
42	SIN3AK20	chr6:140392186-140392562	SK-N-SH	brain:	n/a	n/a
43	SMC3	chr6:140391927-140393351	Hela-S3	cervix:	n/a	n/a
44	SRF	chr6:140392066-140392657	MCF-7	breast:	n/a	chr6:140392362-140392373 chr6:140392360-140392374 chr6:140392362-140392375 chr6:140392360-140392377 chr6:140392364-140392373 chr6:140392363-140392377 chr6:140392362-140392375 chr6:140392363-140392374
45	SRF	chr6:140392071-140392661	MCF-7	breast:	n/a	chr6:140392362-140392373 chr6:140392360-140392374 chr6:140392362-140392375 chr6:140392360-140392377 chr6:140392364-140392373 chr6:140392363-140392377 chr6:140392362-140392375 chr6:140392363-140392374
46	STAT3	chr6:140390129-140390153	MCF10A-Er-Src	breast:	n/a	n/a
47	TAF1	chr6:140392187-140392646	PFSK-1	brain:	n/a	n/a
48	TCF12	chr6:140391916-140393622	SK-N-SH	brain:	n/a	chr6:140393598-140393607
49	TCF12	chr6:140391848-140393607	SK-N-SH	brain:	n/a	chr6:140393598-140393607
50	TCF7L2	chr6:140390272-140390558	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:140388648..140390950-chr6:140391151..140393468,2	MCF-7	breast:
2	chr6:140390060..140392664-chr6:140397671..140399616,2	MCF-7	breast:
3	chr6:140390402..140393143-chr6:140395064..140396701,2	MCF-7	breast:
4	chr6:139695731..139697417-chr6:140391415..140394003,2	MCF-7	breast:
5	chr6:140385652..140387203-chr6:140390391..140391912,2	K562	blood:
6	chr6:140388648..140390950-chr6:140391151..140393468,2	MCF-7	breast:
7	chr6:139692663..139698708-chr6:140381231..140386402,5	MCF-7	breast:
8	chr6:140385652..140387203-chr6:140390391..140391912,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HECA-3	chr6:140388574-140388777	XLOC_005485
2	lnc-HECA-3	chr6:140388572-140389017	XLOC_005485
3	lnc-HECA-3	chr6:140388571-140389212	NONHSAT115266
4	lnc-HECA-3	chr6:140388574-140389017	XLOC_005485
5	lnc-HECA-3	chr6:140388587-140389017	XLOC_005485

Variant related genes	Relation type
ENSG00000236013	TF binding region
ENSG00000164442	chromatin interactions
PRDM16	miRNA target sites

Extended variants
information (count: 225 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:225 , 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	rs371488866	chr6:140385391-140385392	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs58121204	chr6:140385393-140385394	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs181937009	chr6:140385395-140385396	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs186583755	chr6:140385397-140385398	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs191821826	chr6:140385399-140385400	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs11962138	chr6:140385412-140385413	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs58517957	chr6:140385423-140385424	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs143442561	chr6:140385425-140385426	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs367752270	chr6:140385500-140385501	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs183382543	chr6:140385669-140385670	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs540913462	chr6:140385682-140385683	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs114524238	chr6:140385703-140385704	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs574865955	chr6:140385752-140385753	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs75672208	chr6:140385767-140385768	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs563360559	chr6:140385808-140385809	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs143931275	chr6:140385826-140385827	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs375579664	chr6:140385828-140385829	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs564487408	chr6:140385832-140385833	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs148222984	chr6:140385879-140385880	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs546912732	chr6:140385960-140385961	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs186192964	chr6:140385969-140385970	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs553843450	chr6:140385982-140385983	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs11155102	chr6:140386022-140386023	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs189773652	chr6:140386099-140386100	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs10627089	chr6:140386113-140386114	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs377096554	chr6:140386114-140386115	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs201277353	chr6:140386116-140386117	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs111624910	chr6:140386125-140386126	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs545647065	chr6:140386126-140386127	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs536995656	chr6:140386128-140386129	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs58721800	chr6:140386151-140386152	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs71549060	chr6:140386154-140386155	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs558579923	chr6:140386239-140386240	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs182103973	chr6:140386246-140386247	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs577249018	chr6:140386265-140386266	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs188264539	chr6:140386295-140386296	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs9389740	chr6:140386411-140386412	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs150666320	chr6:140386424-140386425	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs530577306	chr6:140386448-140386449	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs192550077	chr6:140386464-140386465	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs541970957	chr6:140386473-140386474	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs78948484	chr6:140386532-140386533	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs183230088	chr6:140386584-140386585	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs188569949	chr6:140386592-140386593	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs564125081	chr6:140386618-140386619	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs140147389	chr6:140386625-140386626	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs143878838	chr6:140386636-140386637	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs562159247	chr6:140386649-140386650	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs373597611	chr6:140386676-140386677	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs77654938	chr6:140386691-140386692	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Autism	22495311	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Gastric cancer	17908304	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	19010834	CNVD
Non-small cell lung cancer	21044232	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21385341	CNVD
Prostate cancer	16705090	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Colorectal cancer	16272173	CNVD
Ependymoma	16718352	CNVD
High-proliferative meningiomas	17937814	CNVD
Intracranial tumor	16823260	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Zellweger syndrome	21572526	CNVD
Follicular lymphoma	20505157	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Malignant melanoma	18718029	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Breast cancer	17603634	CNVD
Chondromyxoid Fibroma	20696777	CNVD
Cancer	21183584	CNVD
Developmental delay	19490664	CNVD
Burkitt''s lymphoma	18698080	CNVD
Follicular lymphoma	18703704	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Adenoid cystic carcinoma	18698036	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Leukemia	18688285	CNVD
Breast cancer	21364760	CNVD
Renal cell carcinoma	18592004	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Malignant melanoma	17260012	CNVD
Prostate cancer	18632612	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute monocytic leukemia	16498392	CNVD
Endocrine pancreatic tumor	17914106	CNVD
Soft tissue tumor	16732325	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
craniofacial dysmorphism	21918468	CNVD

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140380000-140385800	Enhancers	NHDF-Ad	bronchial
2	chr6:140380600-140386400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:140381200-140385800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:140382400-140386400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:140383200-140385600	Weak transcription	Ovary	ovary
6	chr6:140384200-140385800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:140384200-140391400	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:140384400-140385800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:140384400-140385800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr6:140384400-140389600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:140384400-140391800	Weak transcription	Fetal Stomach	stomach
12	chr6:140384400-140391800	Weak transcription	Stomach Mucosa	stomach
13	chr6:140384400-140392800	Weak transcription	Aorta	Aorta
14	chr6:140384600-140385600	Weak transcription	Fetal Intestine Large	intestine
15	chr6:140384600-140385600	Weak transcription	Fetal Intestine Small	intestine
16	chr6:140384600-140391200	Weak transcription	Fetal Lung	lung
17	chr6:140384600-140392000	Weak transcription	HSMMtube	muscle
18	chr6:140384600-140392200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:140384600-140394000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:140384800-140385600	Weak transcription	Adipose Nuclei	Adipose
21	chr6:140385000-140385400	Weak transcription	NHLF	lung
22	chr6:140385000-140389800	Weak transcription	Osteobl	bone
23	chr6:140385200-140390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:140385200-140391200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:140385400-140385600	Enhancers	NHLF	lung
26	chr6:140385600-140385800	Enhancers	Adipose Nuclei	Adipose
27	chr6:140385600-140386000	Enhancers	Fetal Intestine Large	intestine
28	chr6:140385600-140386000	Enhancers	Fetal Intestine Small	intestine
29	chr6:140385600-140386000	Enhancers	Ovary	ovary
30	chr6:140385600-140390200	Weak transcription	NHLF	lung
31	chr6:140385800-140386400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:140385800-140390000	Weak transcription	NHDF-Ad	bronchial
33	chr6:140385800-140391000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:140385800-140391200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:140385800-140391800	Weak transcription	Adipose Nuclei	Adipose
36	chr6:140386000-140391000	Weak transcription	Ovary	ovary
37	chr6:140386000-140392200	Weak transcription	Fetal Intestine Small	intestine
38	chr6:140386200-140386400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:140386200-140386800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr6:140386400-140386800	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr6:140386400-140388000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:140388000-140388200	Enhancers	Placenta Amnion	Placenta Amnion
43	chr6:140389600-140390400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:140389800-140390000	Enhancers	Osteobl	bone
45	chr6:140390000-140390400	Weak transcription	Osteobl	bone
46	chr6:140390000-140395400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:140390000-140395400	Enhancers	NHDF-Ad	bronchial
48	chr6:140390200-140395400	Enhancers	NHLF	lung
49	chr6:140390400-140391800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:140390400-140395000	Enhancers	Osteobl	bone

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