Variant report

Variant	nsv593079
Chromosome Location	chr3:196055365-196062115
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr3:196057273-196057440	K562	blood:	n/a	n/a
2	FOXA1	chr3:196057526-196057829	HepG2	liver:	n/a	n/a
3	FOXA2	chr3:196057568-196057707	HepG2	liver:	n/a	n/a
4	IRF1	chr3:196055372-196055376	K562	blood:	n/a	n/a
5	POLR2A	chr3:196057521-196057705	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:196055687-196055695	K562	blood:	n/a	n/a
7	POLR2A	chr3:196061805-196061860	K562	blood:	n/a	n/a
8	POLR2A	chr3:196057167-196057257	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:196055216-196055510	MCF10A-Er-Src	breast:	n/a	n/a
10	ZNF384	chr3:196059690-196059781	K562	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:196012576..196016636-chr3:196061383..196069148,11	K562	blood:
2	chr3:196054797..196056651-chr3:196089177..196091738,2	K562	blood:
3	chr3:196043658..196046454-chr3:196052736..196055681,2	MCF-7	breast:
4	chr3:196054872..196057138-chr3:196227517..196230475,2	K562	blood:
5	chr3:196053196..196055442-chr3:196068574..196070294,2	MCF-7	breast:
6	chr3:196043597..196046565-chr3:196058227..196060990,3	K562	blood:
7	chr3:196043015..196046706-chr3:196061951..196066451,7	K562	blood:
8	chr3:196046919..196051231-chr3:196053241..196055569,4	K562	blood:
9	chr3:196049252..196052766-chr3:196054178..196057150,4	K562	blood:
10	chr3:196043015..196047197-chr3:196061951..196068288,11	K562	blood:
11	chr3:196014212..196016306-chr3:196062015..196064940,3	MCF-7	breast:
12	chr3:196039550..196042176-chr3:196054293..196056157,2	K562	blood:
13	chr3:196044943..196046563-chr3:196056014..196058811,2	MCF-7	breast:
14	chr3:196057685..196059203-chr3:196062080..196064140,2	MCF-7	breast:
15	chr3:196013231..196016156-chr3:196060060..196062117,2	MCF-7	breast:
16	chr3:196043597..196046330-chr3:196059490..196061514,2	K562	blood:
17	chr3:196057685..196059203-chr3:196062080..196064140,2	MCF-7	breast:

No data

Variant related genes	Relation type
TM4SF19	TF binding region
ENSG00000161217	chromatin interactions
ENSG00000272741	chromatin interactions
ENSG00000213123	chromatin interactions
ENSG00000212146	chromatin interactions
ENSG00000235897	chromatin interactions
ENSG00000145107	chromatin interactions

Extended variants
information (count: 280 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:280 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12636849	chr3:196055365-196055366	Weak transcription Enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
2	rs185366261	chr3:196055424-196055425	Weak transcription Enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs563764808	chr3:196055592-196055593	Weak transcription Enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs531864826	chr3:196055605-196055606	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs550076002	chr3:196055611-196055612	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs568284533	chr3:196055714-196055715	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs138132591	chr3:196055749-196055750	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs142625155	chr3:196055751-196055752	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs566771658	chr3:196055777-196055778	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs566156063	chr3:196055816-196055817	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs811271	chr3:196055878-196055879	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs534467857	chr3:196055881-196055882	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs539594822	chr3:196055904-196055905	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs34061826	chr3:196055918-196055919	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs769599	chr3:196055940-196055941	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs74557486	chr3:196055952-196055953	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs113681876	chr3:196055971-196055972	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs113548058	chr3:196055975-196055976	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs368256182	chr3:196055976-196055977	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs538104555	chr3:196056004-196056005	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs556520340	chr3:196056014-196056015	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs574502510	chr3:196056015-196056016	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs549057179	chr3:196056065-196056066	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs549418874	chr3:196056072-196056073	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs182744882	chr3:196056093-196056094	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs577761793	chr3:196056096-196056097	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs187409724	chr3:196056105-196056106	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs567801470	chr3:196056147-196056148	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs115404653	chr3:196056157-196056158	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs545525285	chr3:196056213-196056214	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs201363631	chr3:196056293-196056294	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs34061392	chr3:196056295-196056296	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs201121427	chr3:196056319-196056320	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs191959281	chr3:196056492-196056493	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs531225492	chr3:196056529-196056530	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs538095423	chr3:196056531-196056532	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
37	rs556627321	chr3:196056673-196056674	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs550014561	chr3:196056740-196056741	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs572956021	chr3:196056748-196056749	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs183016945	chr3:196056756-196056757	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
41	rs374120629	chr3:196056767-196056768	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs12637717	chr3:196056806-196056807	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
43	rs562413637	chr3:196056835-196056836	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs529600199	chr3:196056836-196056837	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs187526264	chr3:196056839-196056840	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs71323714	chr3:196056846-196056847	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs539906315	chr3:196056899-196056900	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs557701503	chr3:196056915-196056916	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
49	rs569125455	chr3:196056944-196056945	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
50	rs572759509	chr3:196056971-196056972	Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Chronic lymphocytic leukemia	20421269	CNVD

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196047600-196063600	Weak transcription	NHEK	skin
2	chr3:196051000-196057200	Weak transcription	Hela-S3	cervix
3	chr3:196051400-196063600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:196052000-196062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:196054000-196055600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:196054400-196056400	Weak transcription	Pancreas	Pancrea
7	chr3:196054600-196061800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:196054600-196091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:196054800-196060800	Weak transcription	K562	blood
10	chr3:196054800-196064400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:196057200-196057800	Strong transcription	Hela-S3	cervix
12	chr3:196057800-196062600	Weak transcription	Hela-S3	cervix
13	chr3:196059800-196060000	Enhancers	Esophagus	oesophagus
14	chr3:196060200-196062600	Weak transcription	Esophagus	oesophagus
15	chr3:196060800-196061000	Enhancers	K562	blood
16	chr3:196061000-196061200	Genic enhancers	K562	blood
17	chr3:196061200-196062400	Weak transcription	K562	blood
18	chr3:196061800-196063000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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