Variant report

Variant	nsv3719
Chromosome Location	chr3:20133243-20150202
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	ATF1	chr3:20145751-20146090	K562	blood:	n/a	n/a
2	ATF2	chr3:20145673-20146200	GM12878	blood:	n/a	n/a
3	ATF2	chr3:20145678-20146063	GM12878	blood:	n/a	n/a
4	BHLHE40	chr3:20145419-20146172	GM12878	blood:	n/a	n/a
5	BRCA1	chr3:20139833-20139877	HepG2	liver:	n/a	n/a
6	CEBPB	chr3:20137853-20138186	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr3:20137833-20138154	A549	lung:	n/a	n/a
8	CEBPB	chr3:20137858-20138195	IMR90	lung:	n/a	n/a
9	CEBPB	chr3:20137850-20138180	HepG2	liver:	n/a	n/a
10	CEBPB	chr3:20137924-20138108	K562	blood:	n/a	n/a
11	CREB1	chr3:20145677-20146221	GM12878	blood:	n/a	n/a
12	CREB1	chr3:20145592-20146202	GM12878	blood:	n/a	n/a
13	CTCF	chr3:20146898-20147004	GM12878	blood:	n/a	n/a
14	CTCF	chr3:20141280-20141430	HL-60	blood:	n/a	n/a
15	CTCF	chr3:20149036-20149135	Fibrobl	skin:	n/a	n/a
16	CUX1	chr3:20143981-20144047	GM12878	blood:	n/a	n/a
17	EBF1	chr3:20145696-20146108	GM12878	blood:	n/a	n/a
18	EP300	chr3:20149841-20149915	K562	blood:	n/a	n/a
19	EP300	chr3:20145723-20146124	GM12878	blood:	n/a	chr3:20145822-20145836 chr3:20145732-20145746
20	EP300	chr3:20145710-20146049	GM12878	blood:	n/a	chr3:20145822-20145836 chr3:20145732-20145746 chr3:20145712-20145726
21	FOS	chr3:20137881-20138187	MCF10A-Er-Src	breast:	n/a	n/a
22	FOXA1	chr3:20132735-20133469	HepG2	liver:	n/a	n/a
23	GATA1	chr3:20145781-20146361	PBDE	blood:	n/a	chr3:20146064-20146074 chr3:20145866-20145875
24	GATA2	chr3:20145819-20146177	SH-SY5Y	brain:	n/a	chr3:20146064-20146074 chr3:20145866-20145875
25	GATA3	chr3:20145895-20146195	MCF-7	breast:	n/a	chr3:20146064-20146074
26	GATA3	chr3:20145814-20146267	SK-N-SH	brain:	n/a	chr3:20146064-20146074 chr3:20145866-20145875
27	GATA3	chr3:20145717-20146440	MCF-7	breast:	n/a	chr3:20146064-20146074 chr3:20145866-20145875
28	GATA3	chr3:20145891-20146335	SK-N-SH	brain:	n/a	chr3:20146064-20146074
29	GATA3	chr3:20145770-20146386	MCF-7	breast:	n/a	chr3:20146064-20146074 chr3:20145866-20145875
30	GATA3	chr3:20147706-20147744	SH-SY5Y	brain:	n/a	n/a
31	GATA3	chr3:20145987-20146218	SH-SY5Y	brain:	n/a	chr3:20146064-20146074
32	GATA3	chr3:20150066-20151130	MCF-7	breast:	n/a	n/a
33	JUN	chr3:20144147-20144159	K562	blood:	n/a	n/a
34	MAFK	chr3:20142767-20142891	HepG2	liver:	n/a	n/a
35	MAFK	chr3:20142444-20142548	K562	blood:	n/a	n/a
36	MAX	chr3:20145835-20146172	NB4	blood:	n/a	chr3:20145854-20145863 chr3:20145960-20145970
37	MYC	chr3:20136429-20136575	GM12878	blood:	n/a	n/a
38	MYC	chr3:20137856-20138186	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr3:20145777-20146146	NB4	blood:	n/a	chr3:20145854-20145863 chr3:20145960-20145970
40	NFIC	chr3:20145557-20146103	GM12878	blood:	n/a	n/a
41	NR2F2	chr3:20145870-20146226	MCF-7	breast:	n/a	n/a
42	POLR2A	chr3:20137741-20137804	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr3:20138036-20138287	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr3:20142501-20142792	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr3:20150187-20150246	MCF-7	breast:	n/a	n/a
46	POLR2A	chr3:20146698-20146869	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr3:20141022-20141080	MCF-7	breast:	n/a	n/a
48	POLR2A	chr3:20145752-20146140	HL-60	blood:	n/a	n/a
49	POLR2A	chr3:20145668-20146162	HL-60	blood:	n/a	n/a
50	POLR2A	chr3:20140953-20140974	Gliobla	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:20138475..20140475-chr3:20146667..20148276,2	K562	blood:
2	chr3:20123056..20125408-chr3:20133416..20135559,2	MCF-7	breast:
3	chr3:20131147..20133455-chr3:20135064..20136948,2	K562	blood:
4	chr3:20144778..20146752-chr3:20150014..20154937,5	K562	blood:
5	chr3:20080711..20083286-chr3:20145252..20149084,3	MCF-7	breast:
6	chr3:20131147..20133455-chr3:20135064..20136948,2	K562	blood:
7	chr3:20147447..20149147-chr3:20152117..20154267,2	MCF-7	breast:
8	chr3:20138975..20141320-chr3:20146365..20149046,3	K562	blood:
9	chr3:19987372..19989134-chr3:20145217..20148205,2	MCF-7	breast:
10	chr3:20138975..20141320-chr3:20146365..20149046,3	K562	blood:
11	chr3:20096664..20098215-chr3:20134683..20136839,2	K562	blood:
12	chr3:19986031..19988662-chr3:20137303..20140134,2	MCF-7	breast:
13	chr3:20105530..20108149-chr3:20143893..20147714,3	MCF-7	breast:
14	chr3:20070139..20072649-chr3:20135219..20138030,2	K562	blood:
15	chr3:20133592..20135375-chr3:20142503..20144573,2	K562	blood:
16	chr3:20133592..20135375-chr3:20142503..20144573,2	K562	blood:
17	chr3:20080805..20083716-chr3:20136030..20137757,2	K562	blood:
18	chr3:20079315..20082168-chr3:20133365..20135134,2	K562	blood:
19	chr3:20138475..20140475-chr3:20146667..20148276,2	K562	blood:

Variant related genes	Relation type
KAT2B	TF binding region
ENSG00000163576	chromatin interactions
ENSG00000144566	chromatin interactions
ENSG00000114166	chromatin interactions

Extended variants
information (count: 654 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:654 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs563299323	chr3:20133246-20133247	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs116594469	chr3:20133342-20133343	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs6783444	chr3:20133384-20133385	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs559410415	chr3:20133392-20133393	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs528611430	chr3:20133399-20133400	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs75365538	chr3:20133421-20133422	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs140696434	chr3:20133443-20133444	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs562213463	chr3:20133515-20133516	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs116158633	chr3:20133520-20133521	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs551049103	chr3:20133555-20133556	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs566503068	chr3:20133561-20133562	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs149656091	chr3:20133592-20133593	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs11128936	chr3:20133599-20133600	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs549964210	chr3:20133604-20133605	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs188936909	chr3:20133619-20133620	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs6783552	chr3:20133694-20133695	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs533302422	chr3:20133709-20133710	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs199978857	chr3:20133727-20133728	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs368855701	chr3:20133728-20133729	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs202164686	chr3:20133735-20133736	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs56239971	chr3:20133738-20133739	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs7639181	chr3:20133741-20133742	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs371775631	chr3:20133745-20133746	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs539165869	chr3:20133747-20133748	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs553879350	chr3:20133762-20133763	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs181632906	chr3:20133809-20133810	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs12634506	chr3:20133847-20133848	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs7639282	chr3:20133873-20133874	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs372680812	chr3:20133877-20133878	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs186292920	chr3:20133910-20133911	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs116192285	chr3:20133924-20133925	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs189632188	chr3:20133959-20133960	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs551499444	chr3:20134040-20134041	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs79997344	chr3:20134065-20134066	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs180853978	chr3:20134067-20134068	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs527247551	chr3:20134089-20134090	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs549021649	chr3:20134124-20134125	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs549089376	chr3:20134154-20134155	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs2886463	chr3:20134159-20134160	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs78379434	chr3:20134187-20134188	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs569956713	chr3:20134188-20134189	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs571468347	chr3:20134227-20134228	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs558161456	chr3:20134249-20134250	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs374118051	chr3:20134255-20134256	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs186087891	chr3:20134260-20134261	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs554276799	chr3:20134262-20134263	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs566055058	chr3:20134267-20134268	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs536216026	chr3:20134280-20134281	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs530276982	chr3:20134292-20134293	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs368125825	chr3:20134294-20134295	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:74)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Developmental delay	21147756	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Prostate cancer	19363497	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:491 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20102800-20136800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
3	chr3:20123000-20137000	Weak transcription	Spleen	Spleen
4	chr3:20123000-20138400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:20123000-20140800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:20123000-20153000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:20123200-20136800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:20123200-20136800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:20123200-20136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:20123200-20137000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:20123200-20137200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:20123200-20137200	Weak transcription	Esophagus	oesophagus
13	chr3:20123200-20137200	Weak transcription	Fetal Heart	heart
14	chr3:20123200-20137200	Weak transcription	Left Ventricle	heart
15	chr3:20123200-20137200	Weak transcription	Psoas Muscle	Psoas
16	chr3:20123200-20137200	Weak transcription	Right Ventricle	heart
17	chr3:20123200-20137400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:20123200-20137400	Weak transcription	Gastric	stomach
19	chr3:20123200-20137400	Weak transcription	Pancreas	Pancrea
20	chr3:20123200-20138600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:20123200-20141000	Weak transcription	Stomach Mucosa	stomach
22	chr3:20123200-20153200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:20128200-20136000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:20128200-20136200	Weak transcription	Fetal Thymus	thymus
25	chr3:20128200-20136400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:20128200-20137400	Weak transcription	Aorta	Aorta
27	chr3:20128200-20137400	Weak transcription	Lung	lung
28	chr3:20128200-20175800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:20129600-20137400	Weak transcription	Ovary	ovary
30	chr3:20131200-20135800	Weak transcription	Thymus	Thymus
31	chr3:20131200-20137000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:20131200-20140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:20131400-20137200	Weak transcription	Fetal Intestine Small	intestine
34	chr3:20131400-20137200	Weak transcription	Fetal Stomach	stomach
35	chr3:20131400-20140800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:20131600-20136800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:20131600-20137000	Weak transcription	Adipose Nuclei	Adipose
38	chr3:20131800-20134200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:20131800-20135000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:20131800-20136400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:20131800-20153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:20132000-20133600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:20132000-20135800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:20132000-20136800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:20132200-20133600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:20132200-20134600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:20132200-20135200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:20132200-20135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:20132200-20136600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:20132200-20136800	Weak transcription	Brain Hippocampus Middle	brain

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