Variant report

Variant	nsv590974
Chromosome Location	chr3:90309058-90394328
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:526)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:526 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr3:90366886-90367262	HepG2	liver:	n/a	n/a
2	ATF1	chr3:90354495-90354866	K562	blood:	n/a	n/a
3	ATF1	chr3:90366884-90367261	K562	blood:	n/a	n/a
4	BATF	chr3:90326848-90327084	GM12878	blood:	n/a	n/a
5	BATF	chr3:90377512-90377771	GM12878	blood:	n/a	n/a
6	BATF	chr3:90377613-90377778	GM12878	blood:	n/a	n/a
7	BATF	chr3:90326853-90327190	GM12878	blood:	n/a	n/a
8	BATF	chr3:90354598-90354789	GM12878	blood:	n/a	n/a
9	BATF	chr3:90366984-90367151	GM12878	blood:	n/a	n/a
10	BATF	chr3:90368796-90369032	GM12878	blood:	n/a	n/a
11	BATF	chr3:90368793-90369031	GM12878	blood:	n/a	n/a
12	BCL11A	chr3:90368801-90368998	GM12878	blood:	n/a	n/a
13	BCL11A	chr3:90326854-90327078	GM12878	blood:	n/a	n/a
14	BCL11A	chr3:90366917-90367191	GM12878	blood:	n/a	n/a
15	BCL11A	chr3:90368676-90369097	GM12878	blood:	n/a	n/a
16	BCL11A	chr3:90377614-90377765	GM12878	blood:	n/a	n/a
17	BCL11A	chr3:90377530-90377845	GM12878	blood:	n/a	n/a
18	BCL11A	chr3:90354876-90355114	GM12878	blood:	n/a	n/a
19	BCL11A	chr3:90366984-90367130	H1-hESC	embryonic stem cell:	n/a	n/a
20	BCL11A	chr3:90354492-90354858	GM12878	blood:	n/a	n/a
21	BCL11A	chr3:90326833-90327190	GM12878	blood:	n/a	n/a
22	BHLHE40	chr3:90326853-90327190	HepG2	liver:	n/a	n/a
23	BHLHE40	chr3:90377563-90377847	HepG2	liver:	n/a	n/a
24	BHLHE40	chr3:90392310-90392635	HepG2	liver:	n/a	n/a
25	BHLHE40	chr3:90368673-90369114	HepG2	liver:	n/a	n/a
26	BRCA1	chr3:90344481-90344854	Hela-S3	cervix:	n/a	n/a
27	BRCA1	chr3:90350099-90350299	GM12878	blood:	n/a	n/a
28	CEBPB	chr3:90349067-90349349	A549	lung:	n/a	chr3:90349203-90349214 chr3:90349172-90349183
29	CEBPB	chr3:90318894-90319094	A549	lung:	n/a	chr3:90318957-90318968
30	CEBPB	chr3:90349043-90349364	HepG2	liver:	n/a	chr3:90349203-90349214 chr3:90349172-90349183
31	CEBPB	chr3:90366888-90367262	H1-hESC	embryonic stem cell:	n/a	n/a
32	CEBPB	chr3:90318944-90319029	HepG2	liver:	n/a	chr3:90318957-90318968
33	CEBPB	chr3:90354308-90354863	HepG2	liver:	n/a	n/a
34	CEBPD	chr3:90366925-90367205	K562	blood:	n/a	n/a
35	CEBPD	chr3:90326931-90327206	K562	blood:	n/a	n/a
36	CHD1	chr3:90366887-90367262	H1-hESC	embryonic stem cell:	n/a	n/a
37	CHD1	chr3:90392513-90392712	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:90366979-90367244	K562	blood:	n/a	n/a
39	CTCF	chr3:90377516-90377869	K562	blood:	n/a	n/a
40	CTCF	chr3:90354989-90355374	MCF-7	breast:	n/a	n/a
41	CTCF	chr3:90326938-90327082	K562	blood:	n/a	n/a
42	CTCF	chr3:90354865-90355053	K562	blood:	n/a	n/a
43	CTCF	chr3:90368763-90369043	K562	blood:	n/a	n/a
44	CTCF	chr3:90368797-90368982	K562	blood:	n/a	n/a
45	CTCF	chr3:90326930-90327188	K562	blood:	n/a	n/a
46	CUX1	chr3:90350100-90350458	GM12878	blood:	n/a	n/a
47	E2F4	chr3:90366885-90367262	MCF10A-Er-Src	breast:	n/a	n/a
48	E2F4	chr3:90366893-90367262	GM12878	blood:	n/a	n/a
49	E2F4	chr3:90376436-90376493	MCF10A-Er-Src	breast:	n/a	n/a
50	E2F4	chr3:90366396-90366409	MCF10A-Er-Src	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:90383506-90383556	AG09309	skin:	n/a
2	chr3:90383403-90383453	NHBE	bronchial:	n/a
3	chr3:90383403-90383453	AG04450	lung:	fetal
4	chr3:90383403-90383453	Hepatocyte	liver:	n/a
5	chr3:90383506-90383556	GM12878	blood:	n/a
6	chr3:90383403-90383453	AG09309	skin:	n/a
7	chr3:90383403-90383453	MCF-7	breast:	n/a
8	chr3:90383506-90383556	IMR90	lung:	fetal
9	chr3:90383506-90383556	GM12892	blood:	n/a
10	chr3:90383403-90383453	NT2-D1	testis:	n/a
11	chr3:90383403-90383453	GM12878	blood:	n/a
12	chr3:90383506-90383556	HRE	kidney:	n/a
13	chr3:90383403-90383453	RPTEC	kidney:	n/a
14	chr3:90383403-90383453	LNCaP	prostate:	n/a
15	chr3:90383403-90383453	SK-N-SH_RA	brain:	n/a
16	chr3:90383506-90383556	HPAEpiC	pulmonary alveolar:	n/a
17	chr3:90383403-90383453	BE2_C	brain:	n/a
18	chr3:90383403-90383453	AG04449	skin:	fetal
19	chr3:90383403-90383453	HCM	heart:	n/a
20	chr3:90383506-90383556	ProgFib	skin:	n/a
21	chr3:90383403-90383453	AG09319	gingival:	n/a
22	chr3:90383403-90383453	HRCEpiC	kidney:	n/a
23	chr3:90383506-90383556	PFSK-1	brain:	n/a
24	chr3:90383403-90383453	MCF10A-Er-Src	breast:	n/a
25	chr3:90383506-90383556	HNPCEpiC	eye:	n/a
26	chr3:90383506-90383556	HMEC	breast:	n/a
27	chr3:90383506-90383556	SK-N-SH	brain:	n/a
28	chr3:90383506-90383556	HEK293	kidney:	embryo
29	chr3:90383506-90383556	AG10803	skin:	n/a
30	chr3:90383506-90383556	SKMC	muscle:	n/a
31	chr3:90383403-90383453	U87	brain:	n/a
32	chr3:90383403-90383453	GM06990	blood:	n/a
33	chr3:90383403-90383453	H1-hESC	embryonic stem cell:	embryo
34	chr3:90383403-90383453	GM19239	blood:	n/a
35	chr3:90383403-90383453	SKMC	muscle:	n/a
36	chr3:90383506-90383556	HIPEpiC	eye:	n/a
37	chr3:90383403-90383453	K562	blood:	n/a
38	chr3:90383506-90383556	NHBE	bronchial:	n/a
39	chr3:90383506-90383556	HEEpiC	esophagus:	n/a
40	chr3:90383506-90383556	SK-N-SH_RA	brain:	n/a
41	chr3:90383403-90383453	HEK293	kidney:	embryo
42	chr3:90383403-90383453	NHDF-neo	bronchial:	n/a
43	chr3:90383403-90383453	SAEC	small airway:	n/a
44	chr3:90383506-90383556	GM19239	blood:	n/a
45	chr3:90383403-90383453	HEEpiC	esophagus:	n/a
46	chr3:90383506-90383556	ovcar-3	ovarian:	n/a
47	chr3:90383506-90383556	NHDF-neo	bronchial:	n/a
48	chr3:90383506-90383556	Caco-2	colon:	n/a
49	chr3:90383403-90383453	HCF	heart:	n/a
50	chr3:90383403-90383453	SK-N-SH	brain:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CGGBP1-4	chr3:90310564-90310858	NONHSAT090715

No data

Variant related genes	Relation type
PROSP	TF binding region
HSPE1P19	TF binding region
PROSP	CpG island
HSPE1P19	CpG island

Extended variants
information (count: 5334 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:5334 , 50 per page) page: 1 2 3 4 5 6 7 ... 107

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs150337936	chr3:90310612-90310613	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs544769971	chr3:90310613-90310614	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs551224550	chr3:90310618-90310619	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs565040263	chr3:90310686-90310687	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs138135355	chr3:90310695-90310696	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs569418704	chr3:90310701-90310702	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs187317445	chr3:90310706-90310707	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs552048963	chr3:90310709-90310710	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs560815475	chr3:90310712-90310713	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs77001902	chr3:90310715-90310716	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs570355633	chr3:90310754-90310755	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs546519014	chr3:90310781-90310782	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs79945446	chr3:90310795-90310796	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs77628053	chr3:90310801-90310802	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs79602726	chr3:90310809-90310810	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs560104837	chr3:90310810-90310811	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs532415613	chr3:90310836-90310837	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs576995617	chr3:90312058-90312059	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs182028377	chr3:90312066-90312067	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs370480538	chr3:90312068-90312069	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs373924010	chr3:90312072-90312073	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs185844692	chr3:90312078-90312079	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs144482856	chr3:90312098-90312099	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs147965894	chr3:90312101-90312102	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs534630460	chr3:90312117-90312118	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs141025933	chr3:90312119-90312120	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs182943603	chr3:90312127-90312128	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs146167366	chr3:90312134-90312135	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs139687708	chr3:90312135-90312136	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs187487621	chr3:90312152-90312153	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs574714942	chr3:90312154-90312155	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs141852228	chr3:90312160-90312161	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs200957014	chr3:90312163-90312164	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs139829275	chr3:90312164-90312165	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs572703780	chr3:90312204-90312205	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs80254499	chr3:90312225-90312226	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs77248540	chr3:90312230-90312231	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs79650766	chr3:90312234-90312235	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs77541101	chr3:90312238-90312239	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs541567219	chr3:90312257-90312258	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs553813059	chr3:90312421-90312422	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs34348314	chr3:90312432-90312433	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs533521727	chr3:90312434-90312435	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs541955683	chr3:90312439-90312440	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs55710482	chr3:90312442-90312443	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs551797476	chr3:90312447-90312448	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs570620455	chr3:90312452-90312453	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs183084317	chr3:90312500-90312501	ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs187537978	chr3:90312501-90312502	ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs576276982	chr3:90312518-90312519	ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
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
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Soft tissue tumor	16732325	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Lung cancer	19547694	CNVD
Cancer	20164919	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22522925	CNVD
Acute lymphoblastic leukemia	18458336	CNVD

Chromatin state (count:234 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:90312400-90313600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:90312400-90314000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:90314000-90317400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:90317400-90318600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:90320400-90322800	ZNF genes & repeats	Liver	Liver
6	chr3:90320600-90323000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
7	chr3:90320800-90325600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:90321000-90321200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:90321000-90321200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:90321000-90321200	ZNF genes & repeats	Brain Angular Gyrus	brain
11	chr3:90321000-90321200	ZNF genes & repeats	Fetal Lung	lung
12	chr3:90321000-90324000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
13	chr3:90322000-90323800	ZNF genes & repeats	Dnd41	blood
14	chr3:90322200-90322600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:90322200-90322800	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr3:90322200-90323200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr3:90323600-90324000	ZNF genes & repeats	Psoas Muscle	Psoas
18	chr3:90325800-90326400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
19	chr3:90330400-90332200	Enhancers	Dnd41	blood
20	chr3:90330600-90332000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:90331200-90333600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
22	chr3:90332800-90333400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:90333400-90333600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:90336000-90338000	ZNF genes & repeats	Liver	Liver
25	chr3:90336800-90338000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
26	chr3:90337600-90338000	ZNF genes & repeats	Brain Hippocampus Middle	brain
27	chr3:90337800-90342800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:90339800-90340600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr3:90340000-90342600	ZNF genes & repeats	Liver	Liver
30	chr3:90340400-90340600	ZNF genes & repeats	Dnd41	blood
31	chr3:90341400-90345200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr3:90341800-90343000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
33	chr3:90342000-90342800	Active TSS	Right Atrium	heart
34	chr3:90342400-90342800	Active TSS	Aorta	Aorta
35	chr3:90342800-90345200	Weak transcription	Right Atrium	heart
36	chr3:90343800-90347400	Enhancers	Dnd41	blood
37	chr3:90344800-90346400	Weak transcription	Psoas Muscle	Psoas
38	chr3:90345200-90345400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:90345200-90345600	Active TSS	Right Atrium	heart
40	chr3:90346400-90347200	Active TSS	Psoas Muscle	Psoas
41	chr3:90347400-90347600	Weak transcription	Dnd41	blood
42	chr3:90347600-90348800	ZNF genes & repeats	Dnd41	blood
43	chr3:90349800-90350600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
44	chr3:90350000-90350400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr3:90350000-90350400	ZNF genes & repeats	Adipose Nuclei	Adipose
46	chr3:90350000-90350400	Active TSS	Aorta	Aorta
47	chr3:90350200-90350400	ZNF genes & repeats	Primary T cells from cord blood	blood
48	chr3:90350200-90350600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:90351400-90352400	Enhancers	Dnd41	blood
50	chr3:90354000-90355800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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