Variant report

Variant	nsv590972
Chromosome Location	chr3:90264768-90391674
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:551)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:551 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

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	chr3:90368793-90369031	GM12878	blood:	n/a	n/a
5	BATF	chr3:90377613-90377778	GM12878	blood:	n/a	n/a
6	BATF	chr3:90368796-90369032	GM12878	blood:	n/a	n/a
7	BATF	chr3:90326848-90327084	GM12878	blood:	n/a	n/a
8	BATF	chr3:90354598-90354789	GM12878	blood:	n/a	n/a
9	BATF	chr3:90326853-90327190	GM12878	blood:	n/a	n/a
10	BATF	chr3:90377512-90377771	GM12878	blood:	n/a	n/a
11	BATF	chr3:90366984-90367151	GM12878	blood:	n/a	n/a
12	BCL11A	chr3:90366917-90367191	GM12878	blood:	n/a	n/a
13	BCL11A	chr3:90368801-90368998	GM12878	blood:	n/a	n/a
14	BCL11A	chr3:90366984-90367130	H1-hESC	embryonic stem cell:	n/a	n/a
15	BCL11A	chr3:90377530-90377845	GM12878	blood:	n/a	n/a
16	BCL11A	chr3:90354876-90355114	GM12878	blood:	n/a	n/a
17	BCL11A	chr3:90354492-90354858	GM12878	blood:	n/a	n/a
18	BCL11A	chr3:90368676-90369097	GM12878	blood:	n/a	n/a
19	BCL11A	chr3:90326833-90327190	GM12878	blood:	n/a	n/a
20	BCL11A	chr3:90377614-90377765	GM12878	blood:	n/a	n/a
21	BCL11A	chr3:90326854-90327078	GM12878	blood:	n/a	n/a
22	BHLHE40	chr3:90368673-90369114	HepG2	liver:	n/a	n/a
23	BHLHE40	chr3:90377563-90377847	HepG2	liver:	n/a	n/a
24	BHLHE40	chr3:90326853-90327190	HepG2	liver:	n/a	n/a
25	BRCA1	chr3:90344481-90344854	Hela-S3	cervix:	n/a	n/a
26	BRCA1	chr3:90350099-90350299	GM12878	blood:	n/a	n/a
27	CEBPB	chr3:90366888-90367262	H1-hESC	embryonic stem cell:	n/a	n/a
28	CEBPB	chr3:90318944-90319029	HepG2	liver:	n/a	chr3:90318957-90318968
29	CEBPB	chr3:90349067-90349349	A549	lung:	n/a	chr3:90349203-90349214 chr3:90349172-90349183
30	CEBPB	chr3:90349043-90349364	HepG2	liver:	n/a	chr3:90349203-90349214 chr3:90349172-90349183
31	CEBPB	chr3:90290768-90290930	HepG2	liver:	n/a	chr3:90290816-90290827 chr3:90290817-90290828 chr3:90290816-90290829
32	CEBPB	chr3:90290761-90290889	A549	lung:	n/a	chr3:90290816-90290827 chr3:90290817-90290828 chr3:90290816-90290829
33	CEBPB	chr3:90290589-90291029	Hela-S3	cervix:	n/a	chr3:90290816-90290827 chr3:90290817-90290828 chr3:90290816-90290829
34	CEBPB	chr3:90318894-90319094	A549	lung:	n/a	chr3:90318957-90318968
35	CEBPB	chr3:90286746-90286807	IMR90	lung:	n/a	n/a
36	CEBPB	chr3:90354308-90354863	HepG2	liver:	n/a	n/a
37	CEBPD	chr3:90366925-90367205	K562	blood:	n/a	n/a
38	CEBPD	chr3:90326931-90327206	K562	blood:	n/a	n/a
39	CHD1	chr3:90366887-90367262	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr3:90281169-90281226	GM13976	blood:	n/a	n/a
41	CTCF	chr3:90281600-90281750	GM12866	blood:	n/a	n/a
42	CTCF	chr3:90366979-90367244	K562	blood:	n/a	n/a
43	CTCF	chr3:90354865-90355053	K562	blood:	n/a	n/a
44	CTCF	chr3:90280564-90280700	Hela-S3	cervix:	n/a	chr3:90280619-90280640
45	CTCF	chr3:90368797-90368982	K562	blood:	n/a	n/a
46	CTCF	chr3:90326930-90327188	K562	blood:	n/a	n/a
47	CTCF	chr3:90280560-90280710	HMEC	breast:	n/a	chr3:90280619-90280640
48	CTCF	chr3:90269731-90269813	GM13976	blood:	n/a	n/a
49	CTCF	chr3:90280621-90280673	LNCaP	prostate:	n/a	n/a
50	CTCF	chr3:90294833-90294899	Lung_OC	lung:	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	HCF	heart:	n/a
2	chr3:90383506-90383556	HCT-116	colon:	n/a
3	chr3:90383403-90383453	HPAEpiC	pulmonary alveolar:	n/a
4	chr3:90383506-90383556	MCF-7	breast:	n/a
5	chr3:90383506-90383556	NB4	blood:	n/a
6	chr3:90383506-90383556	CMK	blood:	n/a
7	chr3:90383506-90383556	SK-N-SH_RA	brain:	n/a
8	chr3:90383506-90383556	AG09309	skin:	n/a
9	chr3:90383506-90383556	NT2-D1	testis:	n/a
10	chr3:90383403-90383453	SAEC	small airway:	n/a
11	chr3:90383403-90383453	K562	blood:	n/a
12	chr3:90383506-90383556	ovcar-3	ovarian:	n/a
13	chr3:90383403-90383453	HepG2	liver:	n/a
14	chr3:90383403-90383453	HEEpiC	esophagus:	n/a
15	chr3:90383403-90383453	Caco-2	colon:	n/a
16	chr3:90383403-90383453	HCM	heart:	n/a
17	chr3:90383506-90383556	GM12878	blood:	n/a
18	chr3:90383506-90383556	Caco-2	colon:	n/a
19	chr3:90383506-90383556	AG09319	gingival:	n/a
20	chr3:90383403-90383453	GM12878	blood:	n/a
21	chr3:90383403-90383453	ECC-1	luminal epithelium:	n/a
22	chr3:90383506-90383556	LNCaP	prostate:	n/a
23	chr3:90383403-90383453	AG09319	gingival:	n/a
24	chr3:90383506-90383556	ECC-1	luminal epithelium:	n/a
25	chr3:90383506-90383556	GM12891	blood:	n/a
26	chr3:90383506-90383556	NHDF-neo	bronchial:	n/a
27	chr3:90383506-90383556	NHBE	bronchial:	n/a
28	chr3:90383403-90383453	Hepatocyte	liver:	n/a
29	chr3:90383403-90383453	IMR90	lung:	fetal
30	chr3:90383506-90383556	HAEpiC	amniotic membrane:	n/a
31	chr3:90383403-90383453	HCT-116	colon:	n/a
32	chr3:90383403-90383453	HRE	kidney:	n/a
33	chr3:90383506-90383556	SKMC	muscle:	n/a
34	chr3:90383506-90383556	HepG2	liver:	n/a
35	chr3:90383403-90383453	PFSK-1	brain:	n/a
36	chr3:90383506-90383556	ProgFib	skin:	n/a
37	chr3:90383506-90383556	RPTEC	kidney:	n/a
38	chr3:90383403-90383453	H1-hESC	embryonic stem cell:	embryo
39	chr3:90383506-90383556	HL-60	blood:	n/a
40	chr3:90383506-90383556	NH-A	brain:	n/a
41	chr3:90383506-90383556	Jurkat	blood:	n/a
42	chr3:90383403-90383453	SK-N-SH_RA	brain:	n/a
43	chr3:90383506-90383556	AoSMC	blood vessel:	n/a
44	chr3:90383506-90383556	H1-hESC	embryonic stem cell:	embryo
45	chr3:90383403-90383453	NHDF-neo	bronchial:	n/a
46	chr3:90383403-90383453	MCF-7	breast:	n/a
47	chr3:90383506-90383556	T-47D	breast:	n/a
48	chr3:90383403-90383453	U87	brain:	n/a
49	chr3:90383403-90383453	CMK	blood:	n/a
50	chr3:90383403-90383453	HCF	heart:	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: 5498 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:5498 , 50 per page) page: 1 2 3 4 5 6 7 ... 110

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs189056844	chr3:90271011-90271012	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs533292393	chr3:90271038-90271039	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs193266942	chr3:90271060-90271061	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs570197568	chr3:90271063-90271064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs536107647	chr3:90271065-90271066	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs549705088	chr3:90271098-90271099	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs372144865	chr3:90271106-90271107	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs185396618	chr3:90271120-90271121	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs533786421	chr3:90271157-90271158	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs144482807	chr3:90271174-90271175	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs578077303	chr3:90271196-90271197	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs576992893	chr3:90271197-90271198	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs539197579	chr3:90271221-90271222	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs146648811	chr3:90271229-90271230	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs190241054	chr3:90271272-90271273	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs545376697	chr3:90271278-90271279	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs555255470	chr3:90271283-90271284	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs572041296	chr3:90271304-90271305	Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs141206990	chr3:90271436-90271437	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs62277721	chr3:90271452-90271453	Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs533458091	chr3:90271468-90271469	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs185617200	chr3:90271471-90271472	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs188471746	chr3:90271526-90271527	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs112208745	chr3:90271533-90271534	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs144946045	chr3:90271535-90271536	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs566360916	chr3:90271538-90271539	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs186156098	chr3:90271557-90271558	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs146788424	chr3:90271561-90271562	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs547414807	chr3:90271576-90271577	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs570361620	chr3:90271582-90271583	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs140483828	chr3:90271615-90271616	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs200589930	chr3:90271660-90271661	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs556006852	chr3:90271682-90271683	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs569795914	chr3:90271770-90271771	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs535275794	chr3:90271790-90271791	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs190626943	chr3:90271794-90271795	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs572004629	chr3:90271816-90271817	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs543093976	chr3:90271890-90271891	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs182413204	chr3:90271895-90271896	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs187173193	chr3:90271909-90271910	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs190800034	chr3:90271911-90271912	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs543873249	chr3:90271991-90271992	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs537087979	chr3:90272035-90272036	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs113697970	chr3:90272082-90272083	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs138028214	chr3:90272088-90272089	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs149518236	chr3:90272094-90272095	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs528753221	chr3:90272095-90272096	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs34120731	chr3:90272096-90272097	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs75058987	chr3:90272148-90272149	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs146153710	chr3:90272157-90272158	Weak transcription Enhancers	n/a	n/a	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:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:90271000-90271200	Enhancers	Brain Hippocampus Middle	brain
2	chr3:90271200-90271600	Active TSS	Brain Hippocampus Middle	brain
3	chr3:90271200-90272200	Enhancers	Brain Substantia Nigra	brain
4	chr3:90271400-90271800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:90271600-90272000	Enhancers	Brain Hippocampus Middle	brain
6	chr3:90271800-90275400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:90275400-90275600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:90275600-90276000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:90276000-90276400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:90282400-90282800	Enhancers	Dnd41	blood
11	chr3:90284200-90284800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:90290800-90291000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:90291000-90291200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:90291000-90291200	Enhancers	Adipose Nuclei	Adipose
15	chr3:90312400-90313600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:90312400-90314000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:90314000-90317400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:90317400-90318600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:90320400-90322800	ZNF genes & repeats	Liver	Liver
20	chr3:90320600-90323000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
21	chr3:90320800-90325600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:90321000-90321200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:90321000-90321200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:90321000-90321200	ZNF genes & repeats	Brain Angular Gyrus	brain
25	chr3:90321000-90321200	ZNF genes & repeats	Fetal Lung	lung
26	chr3:90321000-90324000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
27	chr3:90322000-90323800	ZNF genes & repeats	Dnd41	blood
28	chr3:90322200-90322600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:90322200-90322800	ZNF genes & repeats	Brain Anterior Caudate	brain
30	chr3:90322200-90323200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr3:90323600-90324000	ZNF genes & repeats	Psoas Muscle	Psoas
32	chr3:90325800-90326400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
33	chr3:90330400-90332200	Enhancers	Dnd41	blood
34	chr3:90330600-90332000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:90331200-90333600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
36	chr3:90332800-90333400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:90333400-90333600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:90336000-90338000	ZNF genes & repeats	Liver	Liver
39	chr3:90336800-90338000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
40	chr3:90337600-90338000	ZNF genes & repeats	Brain Hippocampus Middle	brain
41	chr3:90337800-90342800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:90339800-90340600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
43	chr3:90340000-90342600	ZNF genes & repeats	Liver	Liver
44	chr3:90340400-90340600	ZNF genes & repeats	Dnd41	blood
45	chr3:90341400-90345200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:90341800-90343000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr3:90342000-90342800	Active TSS	Right Atrium	heart
48	chr3:90342400-90342800	Active TSS	Aorta	Aorta
49	chr3:90342800-90345200	Weak transcription	Right Atrium	heart
50	chr3:90343800-90347400	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links