Variant report

Variant	nsv517032
Chromosome Location	chr20:16560990-16585314
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	BRCA1	chr20:16577299-16577304	HepG2	liver:	n/a	n/a
2	CEBPB	chr20:16564805-16565026	HepG2	liver:	n/a	chr20:16564925-16564936 chr20:16564924-16564937 chr20:16564924-16564937 chr20:16564924-16564935
3	CEBPB	chr20:16583606-16583847	A549	lung:	n/a	chr20:16583778-16583789
4	CEBPB	chr20:16585006-16585344	HepG2	liver:	n/a	chr20:16585163-16585176 chr20:16585164-16585175
5	CEBPB	chr20:16585117-16585328	Hela-S3	cervix:	n/a	chr20:16585163-16585176 chr20:16585164-16585175
6	CEBPB	chr20:16560803-16561178	IMR90	lung:	n/a	n/a
7	CEBPB	chr20:16560762-16561198	MCF-7	breast:	n/a	n/a
8	CEBPB	chr20:16585034-16585336	IMR90	lung:	n/a	chr20:16585163-16585176 chr20:16585164-16585175
9	CEBPB	chr20:16576176-16576347	HepG2	liver:	n/a	chr20:16576264-16576275
10	CEBPB	chr20:16585011-16585341	A549	lung:	n/a	chr20:16585163-16585176 chr20:16585164-16585175
11	CEBPB	chr20:16560803-16561474	Hela-S3	cervix:	n/a	chr20:16561388-16561401
12	CEBPB	chr20:16583651-16583886	HepG2	liver:	n/a	chr20:16583778-16583789
13	CEBPB	chr20:16585126-16585310	K562	blood:	n/a	chr20:16585163-16585176 chr20:16585164-16585175
14	CHD2	chr20:16569025-16569178	HepG2	liver:	n/a	n/a
15	CTCF	chr20:16570415-16570532	H1-hESC	embryonic stem cell:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
16	CTCF	chr20:16570344-16570630	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
17	CTCF	chr20:16570380-16570530	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
18	CTCF	chr20:16576817-16576849	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr20:16570411-16570534	LNCaP	prostate:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
20	CTCF	chr20:16568460-16568610	MCF-7	breast:	n/a	n/a
21	CTCF	chr20:16568440-16568590	HepG2	liver:	n/a	n/a
22	CTCF	chr20:16570235-16570645	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
23	CTCF	chr20:16570227-16570660	HepG2	liver:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
24	CTCF	chr20:16568153-16568265	MCF-7	breast:	n/a	n/a
25	CTCF	chr20:16561300-16561450	HEEpiC	esophagus:	n/a	n/a
26	CTCF	chr20:16570380-16570530	HEK293	kidney:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
27	CTCF	chr20:16570416-16570519	HepG2	liver:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
28	CTCF	chr20:16570420-16570570	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
29	CTCF	chr20:16570366-16570572	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
30	CTCF	chr20:16570360-16570582	A549	lung:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
31	CTCF	chr20:16570520-16570670	A549	lung:	n/a	n/a
32	CTCF	chr20:16570360-16570510	HepG2	liver:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
33	CTCF	chr20:16570340-16570490	A549	lung:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
34	CTCF	chr20:16571200-16571350	HepG2	liver:	n/a	n/a
35	CTCF	chr20:16561280-16561430	Caco-2	colon:	n/a	n/a
36	CTCF	chr20:16570383-16570554	A549	lung:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
37	CTCF	chr20:16568780-16568930	GM12865	blood:	n/a	n/a
38	CTCF	chr20:16570375-16570553	LNCaP	prostate:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
39	CTCF	chr20:16561340-16561490	HepG2	liver:	n/a	n/a
40	CTCF	chr20:16570363-16570588	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
41	CTCF	chr20:16570358-16570569	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
42	CTCF	chr20:16570353-16570589	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
43	CTCF	chr20:16570320-16570470	A549	lung:	n/a	n/a
44	CTCF	chr20:16570348-16570562	HepG2	liver:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
45	CTCF	chr20:16570355-16570586	MCF-7	breast:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
46	CTCF	chr20:16570400-16570550	HepG2	liver:	n/a	chr20:16570465-16570481 chr20:16570464-16570482 chr20:16570467-16570480 chr20:16570467-16570475
47	E2F4	chr20:16581786-16581793	MCF10A-Er-Src	breast:	n/a	n/a
48	E2F4	chr20:16583572-16584010	MCF10A-Er-Src	breast:	n/a	n/a
49	E2F4	chr20:16560720-16561161	MCF10A-Er-Src	breast:	n/a	n/a
50	EP300	chr20:16560869-16561207	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:16577829..16580516-chr20:16584380..16586339,2	MCF-7	breast:
2	chr20:16570035..16570816-chr20:16741683..16742301,3	MCF-7	breast:
3	chr20:16567323..16569576-chr20:16708073..16710976,2	MCF-7	breast:
4	chr20:16577829..16580516-chr20:16584380..16586339,2	MCF-7	breast:
5	chr20:16550509..16554024-chr20:16560848..16563415,3	MCF-7	breast:
6	chr20:16554484..16557263-chr20:16559352..16563570,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIF16B-6	chr20:16570680-16570827	NONHSAT078737
2	lnc-KIF16B-5	chr20:16566978-16567338	NONHSAT078736
3	lnc-KIF16B-6	chr20:16585193-16585738	NONHSAT078737
4	lnc-KIF16B-6	chr20:16568429-16568467	NONHSAT078737

Variant related genes	Relation type
RPLP0P1	TF binding region
ENSG00000125870	chromatin interactions

Extended variants
information (count: 773 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:773 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2143989	chr20:16560990-16560991	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs536751874	chr20:16561001-16561002	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs181932468	chr20:16561050-16561051	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs535535517	chr20:16561067-16561068	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs74539188	chr20:16561184-16561185	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs534543310	chr20:16561195-16561196	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs997972	chr20:16561203-16561204	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs113594845	chr20:16561209-16561210	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs544869895	chr20:16561210-16561211	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs187012653	chr20:16561222-16561223	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs10706294	chr20:16561233-16561234	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs398081274	chr20:16561236-16561237	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs398088330	chr20:16561237-16561238	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs2235969	chr20:16561290-16561291	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs554409533	chr20:16561298-16561299	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs6514693	chr20:16561360-16561361	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs560852192	chr20:16561389-16561390	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs2235968	chr20:16561391-16561392	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs11700102	chr20:16561395-16561396	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs558169552	chr20:16561427-16561428	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs145485872	chr20:16561431-16561432	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs77269927	chr20:16561454-16561455	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs11700136	chr20:16561484-16561485	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs6044144	chr20:16561487-16561488	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs148825234	chr20:16561549-16561550	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs551246931	chr20:16561559-16561560	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs377145461	chr20:16561564-16561565	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs569529148	chr20:16561587-16561588	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs145203462	chr20:16561616-16561617	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs548549242	chr20:16561648-16561649	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs190601441	chr20:16561701-16561702	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs137946742	chr20:16561702-16561703	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs73901135	chr20:16561703-16561704	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs555311542	chr20:16561708-16561709	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs571069841	chr20:16561721-16561722	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs182083811	chr20:16561798-16561799	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs561581034	chr20:16561824-16561825	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs140878852	chr20:16561839-16561840	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs369569008	chr20:16561856-16561857	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs542284555	chr20:16561893-16561894	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs372843341	chr20:16561905-16561906	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs2328045	chr20:16561909-16561910	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs540287143	chr20:16561937-16561938	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs6034540	chr20:16562000-16562001	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs55776240	chr20:16562007-16562008	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs532797770	chr20:16562043-16562044	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs74927179	chr20:16562051-16562052	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs563074682	chr20:16562065-16562066	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs115153643	chr20:16562105-16562106	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs112026770	chr20:16562106-16562107	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Glaucoma	21310917	CNVD
Alagille syndrome	22470819	CNVD
Lung cancer	16773561	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Myelofibrosis	22110671	CNVD
Kabuki syndrome	21720541	CNVD
Glioblastoma multiforme	22286061	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Neurocytoma	17123091	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	21364760	CNVD
lymphocytic leukemia	21291569	CNVD

Chromatin state (count:142 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16556400-16561000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr20:16556400-16562400	Weak transcription	Left Ventricle	heart
3	chr20:16556600-16561000	Weak transcription	Colonic Mucosa	Colon
4	chr20:16557000-16561000	Weak transcription	Fetal Muscle Leg	muscle
5	chr20:16559400-16562000	Enhancers	Fetal Intestine Large	intestine
6	chr20:16559600-16561200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr20:16559600-16561800	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr20:16559600-16561800	Enhancers	NHDF-Ad	bronchial
9	chr20:16559600-16562000	Enhancers	Duodenum Mucosa	Duodenum
10	chr20:16559600-16562000	Enhancers	Fetal Intestine Small	intestine
11	chr20:16559600-16562200	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr20:16559800-16561000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr20:16559800-16562000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr20:16559800-16562200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr20:16559800-16564600	Enhancers	Fetal Brain Male	brain
16	chr20:16559800-16567000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr20:16560000-16561200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr20:16560000-16561400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr20:16560000-16561600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr20:16560000-16561600	Enhancers	HMEC	breast
21	chr20:16560000-16561800	Enhancers	Osteobl	bone
22	chr20:16560000-16562000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr20:16560000-16562000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr20:16560000-16562000	Enhancers	Stomach Mucosa	stomach
25	chr20:16560000-16562200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:16560000-16562200	Enhancers	NHEK	skin
27	chr20:16560000-16562400	Enhancers	Placenta Amnion	Placenta Amnion
28	chr20:16560000-16562600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr20:16560200-16561000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr20:16560200-16561000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr20:16560200-16561200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr20:16560200-16561200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:16560200-16561200	Weak transcription	Right Atrium	heart
34	chr20:16560200-16561400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr20:16560200-16561400	Enhancers	HSMMtube	muscle
36	chr20:16560200-16561600	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr20:16560200-16561600	Enhancers	Brain Germinal Matrix	brain
38	chr20:16560200-16561600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr20:16560200-16561600	Enhancers	NHLF	lung
40	chr20:16560200-16562200	Enhancers	Fetal Lung	lung
41	chr20:16560400-16561000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr20:16560400-16561200	Weak transcription	Small Intestine	intestine
43	chr20:16560400-16561600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:16560400-16561600	Enhancers	Hela-S3	cervix
45	chr20:16560600-16561000	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr20:16560600-16561200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr20:16560600-16561200	Enhancers	HepG2	liver
48	chr20:16560600-16561400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr20:16560600-16561400	Enhancers	A549	lung
50	chr20:16560600-16561600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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