Variant report

Variant	nsv520805
Chromosome Location	chr3:119359045-119361415
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	CTCF	chr3:119361040-119361190	AoAF	blood vessel:	n/a	n/a
2	E2F4	chr3:119358753-119359127	MCF10A-Er-Src	breast:	n/a	n/a
3	EP300	chr3:119358318-119359242	SK-N-SH	brain:	n/a	chr3:119358549-119358558
4	EP300	chr3:119358518-119359245	SK-N-SH_RA	brain:	n/a	chr3:119358549-119358558
5	EP300	chr3:119355708-119359660	SK-N-SH	brain:	n/a	chr3:119358021-119358035 chr3:119358549-119358558 chr3:119357930-119357938 chr3:119356957-119356971 chr3:119356958-119356972
6	EP300	chr3:119358647-119359227	SK-N-SH_RA	brain:	n/a	n/a
7	GATA2	chr3:119357518-119359232	SH-SY5Y	brain:	n/a	n/a
8	GATA3	chr3:119356512-119359281	SK-N-SH	brain:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
9	GATA3	chr3:119357621-119359298	SH-SY5Y	brain:	n/a	n/a
10	GATA3	chr3:119356390-119359464	SK-N-SH	brain:	n/a	chr3:119357125-119357135 chr3:119357061-119357071
11	JUND	chr3:119358312-119359237	SK-N-SH	brain:	n/a	chr3:119358550-119358558 chr3:119358549-119358558 chr3:119358575-119358587 chr3:119358551-119358558
12	JUND	chr3:119361194-119361394	K562	blood:	n/a	n/a
13	JUND	chr3:119356288-119359356	SK-N-SH	brain:	n/a	chr3:119358550-119358558 chr3:119358549-119358558 chr3:119358575-119358587 chr3:119358551-119358558
14	KAP1	chr3:119360144-119360582	HEK293	kidney:	n/a	n/a
15	MAZ	chr3:119361214-119361377	K562	blood:	n/a	n/a
16	MXI1	chr3:119356499-119359364	SK-N-SH	brain:	n/a	n/a
17	MYC	chr3:119361120-119361556	K562	blood:	n/a	n/a
18	NFIC	chr3:119358399-119359231	SK-N-SH	brain:	n/a	n/a
19	NFIC	chr3:119356328-119359285	GM12878	blood:	n/a	n/a
20	PBX3	chr3:119358372-119359220	SK-N-SH	brain:	n/a	n/a
21	PML	chr3:119356256-119359119	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:119358613-119359270	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr3:119358874-119359169	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr3:119361054-119361279	K562	blood:	n/a	n/a
25	RAD21	chr3:119358868-119359157	SK-N-SH_RA	brain:	n/a	n/a
26	REST	chr3:119359004-119359211	SK-N-SH	brain:	n/a	n/a
27	SETDB1	chr3:119360109-119360645	U2OS	brain:	n/a	n/a
28	TBL1XR1	chr3:119361017-119361298	K562	blood:	n/a	n/a
29	TCF12	chr3:119358323-119359353	SK-N-SH	brain:	n/a	n/a
30	TCF12	chr3:119356402-119359447	SK-N-SH	brain:	n/a	chr3:119357774-119357782

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:119361179-119361229	HEK293	kidney:	embryo
2	chr3:119361179-119361229	SK-N-SH	brain:	n/a
3	chr3:119361179-119361229	SAEC	small airway:	n/a
4	chr3:119361179-119361229	GM12878	blood:	n/a
5	chr3:119361179-119361229	HUVEC	blood vessel:	n/a
6	chr3:119361179-119361229	H1-hESC	embryonic stem cell:	embryo
7	chr3:119361179-119361229	HCF	heart:	n/a
8	chr3:119361179-119361229	AG04449	skin:	fetal
9	chr3:119361179-119361229	A549	lung:	n/a
10	chr3:119361179-119361229	Caco-2	colon:	n/a
11	chr3:119361179-119361229	Hela-S3	cervix:	n/a
12	chr3:119361179-119361229	HMEC	breast:	n/a
13	chr3:119361179-119361229	HRCEpiC	kidney:	n/a
14	chr3:119361179-119361229	GM12892	blood:	n/a
15	chr3:119361179-119361229	GM19239	blood:	n/a
16	chr3:119361179-119361229	ECC-1	luminal epithelium:	n/a
17	chr3:119361179-119361229	NB4	blood:	n/a
18	chr3:119361179-119361229	HRPEpiC	eye:	n/a
19	chr3:119361179-119361229	U87	brain:	n/a
20	chr3:119361179-119361229	AG09309	skin:	n/a
21	chr3:119361179-119361229	MCF10A-Er-Src	breast:	n/a
22	chr3:119361179-119361229	BE2_C	brain:	n/a
23	chr3:119361179-119361229	ProgFib	skin:	n/a
24	chr3:119361179-119361229	PANC-1	pancreas:	n/a
25	chr3:119361179-119361229	HCM	heart:	n/a
26	chr3:119361179-119361229	NT2-D1	testis:	n/a
27	chr3:119361179-119361229	ovcar-3	ovarian:	n/a
28	chr3:119361179-119361229	HNPCEpiC	eye:	n/a
29	chr3:119361179-119361229	SK-N-SH_RA	brain:	n/a
30	chr3:119361179-119361229	HEEpiC	esophagus:	n/a
31	chr3:119361179-119361229	AoSMC	blood vessel:	n/a
32	chr3:119361179-119361229	SKMC	muscle:	n/a
33	chr3:119361179-119361229	K562	blood:	n/a
34	chr3:119361179-119361229	HIPEpiC	eye:	n/a
35	chr3:119361179-119361229	Jurkat	blood:	n/a
36	chr3:119361179-119361229	GM12891	blood:	n/a
37	chr3:119361179-119361229	RPTEC	kidney:	n/a
38	chr3:119361179-119361229	NHBE	bronchial:	n/a
39	chr3:119361179-119361229	NHDF-neo	bronchial:	n/a
40	chr3:119361179-119361229	PFSK-1	brain:	n/a
41	chr3:119361179-119361229	HRE	kidney:	n/a
42	chr3:119361179-119361229	HCPEpiC	choroid plexus:	n/a
43	chr3:119361179-119361229	SK-N-MC	brain:	n/a
44	chr3:119361179-119361229	AG09319	gingival:	n/a
45	chr3:119361179-119361229	CMK	blood:	n/a
46	chr3:119361179-119361229	AG04450	lung:	fetal
47	chr3:119361179-119361229	LNCaP	prostate:	n/a
48	chr3:119361179-119361229	IMR90	lung:	fetal
49	chr3:119361179-119361229	MCF-7	breast:	n/a
50	chr3:119361179-119361229	T-47D	breast:	n/a

Variant related genes	Relation type
POPDC2	TF binding region
ENSG00000242052	TF binding region
POPDC2	CpG island
ENSG00000242052	CpG island

Extended variants
information (count: 111 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:111 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs571352	chr3:119359045-119359046	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs9865825	chr3:119359074-119359075	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs530162742	chr3:119359114-119359115	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs548303063	chr3:119359156-119359157	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs368313416	chr3:119359166-119359167	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs150516139	chr3:119359190-119359191	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs183164293	chr3:119359217-119359218	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs114744515	chr3:119359227-119359228	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs570747058	chr3:119359248-119359249	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs538081846	chr3:119359263-119359264	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs139440065	chr3:119359266-119359267	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs35256565	chr3:119359280-119359281	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs114203380	chr3:119359296-119359297	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs149854776	chr3:119359317-119359318	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs369098240	chr3:119359366-119359367	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs145888140	chr3:119359390-119359391	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs534950843	chr3:119359396-119359397	Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs565270395	chr3:119359401-119359402	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs553825399	chr3:119359415-119359416	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs192707321	chr3:119359430-119359431	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs544405066	chr3:119359454-119359455	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs566146811	chr3:119359481-119359482	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs563059987	chr3:119359636-119359637	Weak transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs57279952	chr3:119359645-119359646	Weak transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs61594709	chr3:119359647-119359648	Weak transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs530152468	chr3:119359673-119359674	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs535147626	chr3:119359678-119359679	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs548637632	chr3:119359709-119359710	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs1161030	chr3:119359729-119359730	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs113409903	chr3:119359763-119359764	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs527723578	chr3:119359764-119359765	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs139961207	chr3:119359766-119359767	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs369573170	chr3:119359767-119359768	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs199996630	chr3:119359775-119359776	Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs35250943	chr3:119359808-119359809	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs34576810	chr3:119359810-119359811	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs71156761	chr3:119359834-119359835	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs61218316	chr3:119359835-119359836	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs373102548	chr3:119359837-119359838	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs58544690	chr3:119359840-119359841	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs377177903	chr3:119359841-119359842	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs1184742	chr3:119359850-119359851	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs536064785	chr3:119359851-119359852	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs372991905	chr3:119359861-119359862	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs377315224	chr3:119359865-119359866	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs370856790	chr3:119359868-119359869	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs73192016	chr3:119359871-119359872	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs2692617	chr3:119359876-119359877	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs552597959	chr3:119359900-119359901	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs551250575	chr3:119359905-119359906	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

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
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
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Developmental delay	22180640	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
lymphocytic leukemia	21291569	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Glioblastoma multiforme	22286061	CNVD
Neurodevelopmental disorder	22521361	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD

Chromatin state (count:171 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119341400-119364600	Weak transcription	Liver	Liver
2	chr3:119349800-119378800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:119352000-119378600	Weak transcription	Thymus	Thymus
4	chr3:119352600-119367000	Weak transcription	Ovary	ovary
5	chr3:119354000-119387600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:119354800-119360400	Weak transcription	Lung	lung
7	chr3:119355400-119361000	Weak transcription	Pancreas	Pancrea
8	chr3:119356200-119360200	Weak transcription	Primary T cells from cord blood	blood
9	chr3:119356200-119360800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:119356200-119389000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:119356800-119360800	Weak transcription	Aorta	Aorta
12	chr3:119356800-119361400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:119356800-119364800	Weak transcription	Stomach Mucosa	stomach
14	chr3:119356800-119390000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:119356800-119391800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:119356800-119391800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:119357200-119359200	Enhancers	NHDF-Ad	bronchial
18	chr3:119357200-119361800	Weak transcription	A549	lung
19	chr3:119357200-119383800	Weak transcription	Primary B cells from cord blood	blood
20	chr3:119357800-119360000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:119357800-119360200	Weak transcription	Psoas Muscle	Psoas
22	chr3:119357800-119360600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:119357800-119360800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:119357800-119360800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:119357800-119361800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:119357800-119366600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:119357800-119367000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:119357800-119386400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:119358000-119360200	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:119358000-119360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:119358000-119360400	Weak transcription	Fetal Stomach	stomach
32	chr3:119358000-119360800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:119358000-119360800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:119358000-119361000	Weak transcription	Right Ventricle	heart
35	chr3:119358000-119361000	Weak transcription	Spleen	Spleen
36	chr3:119358000-119361800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:119358000-119361800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:119358000-119361800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:119358000-119361800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:119358000-119361800	Weak transcription	NH-A	brain
41	chr3:119358000-119362000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:119358000-119362000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:119358000-119371200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:119358000-119390600	Weak transcription	Brain Anterior Caudate	brain
45	chr3:119358000-119391800	Weak transcription	Colonic Mucosa	Colon
46	chr3:119358200-119359400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:119358200-119361200	Weak transcription	NHLF	lung
48	chr3:119358200-119361400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:119358200-119361400	Weak transcription	HSMMtube	muscle
50	chr3:119358200-119361600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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