Variant report

Variant	esv3329011
Chromosome Location	chr21:41158272-41160991
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	ARID3A	chr21:41160360-41160603	HepG2	liver:	n/a	n/a
2	ARID3A	chr21:41160290-41160508	K562	blood:	n/a	n/a
3	BHLHE40	chr21:41160253-41160679	K562	blood:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
4	BHLHE40	chr21:41160279-41160720	HepG2	liver:	n/a	chr21:41160530-41160543 chr21:41160532-41160541 chr21:41160531-41160540 chr21:41160526-41160547
5	BRCA1	chr21:41160429-41160440	HepG2	liver:	n/a	n/a
6	CCNT2	chr21:41160383-41160650	K562	blood:	n/a	n/a
7	CEBPB	chr21:41160393-41160469	HepG2	liver:	n/a	n/a
8	CHD2	chr21:41160412-41160523	HepG2	liver:	n/a	n/a
9	CTCF	chr21:41160315-41160494	A549	lung:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
10	CTCF	chr21:41160289-41160573	Lung_OC	lung:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
11	CTCF	chr21:41160280-41160557	A549	lung:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
12	CTCF	chr21:41160215-41160747	T-47D	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
13	CTCF	chr21:41160340-41160490	HAc	cerebellar:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
14	CTCF	chr21:41160340-41160490	HUVEC	blood vessel:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
15	CTCF	chr21:41160280-41160430	HMF	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
16	CTCF	chr21:41160360-41160510	HCFaa	heart:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
17	CTCF	chr21:41160276-41160547	HepG2	liver:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
18	CTCF	chr21:41160300-41160450	HA-sp	spinal cord:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
19	CTCF	chr21:41160320-41160470	HRE	kidney:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
20	CTCF	chr21:41160360-41160510	Caco-2	colon:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
21	CTCF	chr21:41160181-41160612	ECC-1	luminal epithelium:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
22	CTCF	chr21:41160262-41160637	T-47D	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
23	CTCF	chr21:41160320-41160470	HMF	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
24	CTCF	chr21:41160037-41160841	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
25	CTCF	chr21:41160340-41160490	HBMEC	blood vessel:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
26	CTCF	chr21:41160062-41160792	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
27	CTCF	chr21:41160329-41160484	Medullo	brain:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
28	CTCF	chr21:41160107-41160660	HCT-116	colon:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
29	CTCF	chr21:41160261-41160578	Pancreas_OC	pancreas:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
30	CTCF	chr21:41160213-41160644	K562	blood:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
31	CTCF	chr21:41160320-41160470	HRPEpiC	eye:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
32	CTCF	chr21:41160280-41160430	HFF-Myc	foreskin:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
33	CTCF	chr21:41160320-41160470	HMEC	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
34	CTCF	chr21:41160240-41160390	WI-38	lung:	n/a	n/a
35	CTCF	chr21:41160300-41160450	GM12873	blood:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
36	CTCF	chr21:41160258-41160598	LNCaP	prostate:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
37	CTCF	chr21:41160231-41160635	Gliobla	brain:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
38	CTCF	chr21:41160340-41160490	AG10803	skin:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
39	CTCF	chr21:41160360-41160510	HAc	cerebellar:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
40	CTCF	chr21:41160300-41160450	HEEpiC	esophagus:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
41	CTCF	chr21:41160340-41160490	HRPEpiC	eye:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
42	CTCF	chr21:41160274-41160622	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
43	CTCF	chr21:41158828-41158862	ProgFib	skin:	n/a	n/a
44	CTCF	chr21:41160233-41160619	MCF-7	breast:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
45	CTCF	chr21:41160320-41160470	AG04450	lung:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
46	CTCF	chr21:41160147-41160748	HCT-116	colon:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
47	CTCF	chr21:41160400-41160550	AG04450	lung:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
48	CTCF	chr21:41160360-41160510	HEK293	kidney:	n/a	chr21:41160400-41160418 chr21:41160402-41160423
49	CTCF	chr21:41160160-41160310	AG04450	lung:	n/a	n/a
50	CTCF	chr21:41160300-41160450	BE2_C	brain:	n/a	chr21:41160400-41160418 chr21:41160402-41160423

No.	Distal block	Cell Line	Cell type
1	chr21:41160001..41160530-chr8:91943940..91944916,2	MCF-7	breast:
2	chr21:41159981..41160860-chr21:41296870..41297616,2	MCF-7	breast:
3	chr21:41160032..41160849-chr21:41490469..41491137,2	MCF-7	breast:
4	chr21:41160348..41160916-chr3:64008916..64009648,2	MCF-7	breast:
5	chr21:41159923..41160524-chr21:41461365..41462346,2	MCF-7	breast:
6	chr21:41159969..41160584-chr21:41227809..41228464,2	MCF-7	breast:
7	chr21:41097352..41098641-chr21:41159794..41160890,6	MCF-7	breast:
8	chr21:41159946..41160938-chr21:41279878..41281257,7	MCF-7	breast:
9	chr20:52556347..52557088-chr21:41160097..41160766,2	MCF-7	breast:
10	chr21:41160053..41161081-chr21:41282734..41283845,12	MCF-7	breast:
11	chr21:41159272..41160801-chr21:41162335..41164635,2	MCF-7	breast:
12	chr21:41159990..41160890-chr21:41235008..41236199,4	MCF-7	breast:
13	chr21:41160023..41160863-chr21:41279931..41280819,2	MCF-7	breast:
14	chr21:41159565..41161270-chr21:41282682..41284025,38	MCF-7	breast:
15	chr21:41160024..41160878-chr21:41233096..41233742,2	MCF-7	breast:
16	chr21:41160054..41160775-chr21:41284759..41285609,3	MCF-7	breast:
17	chr21:41159939..41160492-chr21:42441112..42441880,2	K562	blood:
18	chr21:41160070..41160863-chr21:41223917..41224517,2	MCF-7	breast:
19	chr21:41159912..41160982-chr21:41296603..41297482,6	MCF-7	breast:
20	chr21:41159987..41160858-chr21:41490256..41491059,2	MCF-7	breast:
21	chr21:41159761..41160935-chr21:41492511..41493448,9	MCF-7	breast:
22	chr21:41160001..41160898-chr21:41492571..41493083,2	K562	blood:
23	chr21:41160210..41160951-chr21:41226545..41227182,3	MCF-7	breast:
24	chr21:41159989..41160905-chr21:41238798..41240091,5	MCF-7	breast:
25	chr21:41159977..41160541-chr21:41415064..41415828,3	MCF-7	breast:
26	chr21:41159985..41160557-chr21:41226622..41227128,2	MCF-7	breast:
27	chr21:41159877..41161605-chr21:41224829..41226757,2	MCF-7	breast:
28	chr21:41160021..41160889-chr21:41227496..41228500,10	MCF-7	breast:
29	chr21:41160014..41161121-chr21:41238636..41239761,13	MCF-7	breast:
30	chr21:41159989..41160876-chr21:41491630..41493536,21	MCF-7	breast:

Variant related genes	Relation type
IGSF5	TF binding region
ENSG00000236352	chromatin interactions
ENSG00000183036	chromatin interactions
ENSG00000183067	chromatin interactions
ENSG00000163636	chromatin interactions

Extended variants
information (count: 137 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:137 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs541337194	chr21:41158374-41158375	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs7510012	chr21:41158470-41158471	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs369240429	chr21:41158477-41158478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs373232545	chr21:41158520-41158521	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs529318539	chr21:41158550-41158551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs373768667	chr21:41158551-41158552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs543118979	chr21:41158553-41158554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs376419139	chr21:41158587-41158588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs376756523	chr21:41158603-41158604	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs563017841	chr21:41158649-41158650	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs34200576	chr21:41158654-41158655	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs35949519	chr21:41158658-41158659	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs36131974	chr21:41158669-41158670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs187238821	chr21:41158682-41158683	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs191694715	chr21:41158690-41158691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs369653831	chr21:41158700-41158701	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs551962327	chr21:41158705-41158706	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs36183102	chr21:41158707-41158708	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs12626208	chr21:41158715-41158716	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs527945699	chr21:41158758-41158759	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs548105536	chr21:41158761-41158762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs74169473	chr21:41158762-41158763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs567130151	chr21:41158783-41158784	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs74169472	chr21:41158815-41158816	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs9974128	chr21:41158816-41158817	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs393595	chr21:41158827-41158828	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs436870	chr21:41158849-41158850	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs9974142	chr21:41158854-41158855	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs62406210	chr21:41158858-41158859	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs150727941	chr21:41158861-41158862	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs74905791	chr21:41158874-41158875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs13047032	chr21:41158885-41158886	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs79039224	chr21:41158898-41158899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs374546981	chr21:41158899-41158900	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs9974301	chr21:41158927-41158928	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs79285614	chr21:41158930-41158931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs554875306	chr21:41158939-41158940	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs34022660	chr21:41158952-41158953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs549517537	chr21:41158953-41158954	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs80090900	chr21:41158960-41158961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs573946439	chr21:41158963-41158964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs567293080	chr21:41158965-41158966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs543084371	chr21:41158978-41158979	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs562878305	chr21:41158990-41158991	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs140176905	chr21:41159017-41159018	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs112105834	chr21:41159018-41159019	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs545539967	chr21:41159029-41159030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs568147902	chr21:41159034-41159035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs552579110	chr21:41159042-41159043	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs75609371	chr21:41159044-41159045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Cancer	16751803	CNVD
Medulloblastoma	21979893	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Down syndrome	17412756	CNVD
Down syndrome	17576883	CNVD
Acute promyelocytic leukemia	19109227	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	17387387	CNVD
Renal cell carcinoma	19461508	CNVD
Seminomas	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Prostate cancer	19156837	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
lymphocytic leukemia	21291569	CNVD
Melanoma	18172304	CNVD
Autism	22958593	CNVD
Schizophrenia	22958593	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Wilms tumour	21544195	CNVD
Ewing''s sarcoma	17952124	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Acute myeloid leukemia	16864856	CNVD
Mental retardation	21031080	CNVD
Polymicrogyria	21031080	CNVD
periventricular nodular heterotopia	21031080	CNVD
Myelodysplastic syndrome	21606161	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Autism	18414403	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Breast cancer	21858162	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17899364	CNVD
Down syndrome	20877625	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Prostate cancer	21147910	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Prostate cancer	17245344	CNVD
Prostate cancer	20473283	CNVD
Chordoma	18071362	CNVD
Cancer	20164919	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:41149400-41160400	Weak transcription	Placenta	Placenta
2	chr21:41155000-41160000	Weak transcription	Fetal Heart	heart
3	chr21:41156800-41160800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr21:41160000-41163600	Enhancers	Fetal Heart	heart
5	chr21:41160200-41160400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:41160200-41160400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:41160200-41160400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr21:41160200-41160400	Enhancers	Brain Substantia Nigra	brain
9	chr21:41160200-41160400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr21:41160200-41160400	Enhancers	Fetal Kidney	kidney
11	chr21:41160200-41160400	Enhancers	Stomach Mucosa	stomach
12	chr21:41160200-41160600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr21:41160200-41160600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr21:41160200-41160600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr21:41160200-41160600	Enhancers	Colon Smooth Muscle	Colon
16	chr21:41160200-41160800	Enhancers	Rectal Smooth Muscle	rectum
17	chr21:41160200-41160800	Enhancers	Stomach Smooth Muscle	stomach
18	chr21:41160200-41161400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr21:41160400-41160600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr21:41160400-41160600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr21:41160400-41160600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr21:41160400-41160600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr21:41160400-41160600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr21:41160400-41160600	Enhancers	Brain Cingulate Gyrus	brain
25	chr21:41160400-41160600	Enhancers	Fetal Brain Male	brain
26	chr21:41160400-41160600	Enhancers	Left Ventricle	heart
27	chr21:41160400-41160600	Enhancers	Lung	lung
28	chr21:41160400-41160600	Flanking Active TSS	Stomach Mucosa	stomach
29	chr21:41160400-41160600	Active TSS	NH-A	brain
30	chr21:41160400-41160800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr21:41160400-41160800	Active TSS	Brain Angular Gyrus	brain
32	chr21:41160400-41160800	Enhancers	Brain Germinal Matrix	brain
33	chr21:41160400-41160800	Active TSS	Brain Hippocampus Middle	brain
34	chr21:41160400-41160800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr21:41160400-41160800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr21:41160400-41160800	Active TSS	Fetal Brain Female	brain
37	chr21:41160400-41160800	Enhancers	Fetal Muscle Trunk	muscle
38	chr21:41160400-41160800	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr21:41160400-41160800	Active TSS	A549	lung
40	chr21:41160400-41160800	Enhancers	HMEC	breast
41	chr21:41160400-41161000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr21:41160400-41161000	Flanking Active TSS	Fetal Kidney	kidney
43	chr21:41160400-41161000	Enhancers	Fetal Muscle Leg	muscle
44	chr21:41160400-41161200	Active TSS	Right Ventricle	heart
45	chr21:41160400-41161400	Enhancers	Placenta	Placenta
46	chr21:41160600-41160800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr21:41160600-41160800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr21:41160600-41160800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr21:41160600-41160800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr21:41160600-41160800	Active TSS	Stomach Mucosa	stomach

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