Variant report

Variant	nsv236806
Chromosome Location	chr3:109638554-109647641
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	BCL3	chr3:109645877-109646527	A549	lung:	n/a	n/a
2	BRCA1	chr3:109645781-109646410	Hela-S3	cervix:	n/a	n/a
3	CBX3	chr3:109645772-109646547	HCT-116	colon:	n/a	n/a
4	CBX3	chr3:109645702-109646599	HCT-116	colon:	n/a	n/a
5	CEBPB	chr3:109645987-109646493	A549	lung:	n/a	n/a
6	CEBPB	chr3:109645783-109646595	HCT-116	colon:	n/a	n/a
7	CEBPB	chr3:109645998-109646461	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr3:109641108-109641558	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr3:109645968-109646417	ECC-1	luminal epithelium:	n/a	n/a
10	CEBPB	chr3:109645773-109646686	HCT-116	colon:	n/a	n/a
11	CEBPB	chr3:109645994-109646413	A549	lung:	n/a	n/a
12	CEBPB	chr3:109645841-109646611	A549	lung:	n/a	n/a
13	CEBPB	chr3:109646013-109646487	IMR90	lung:	n/a	n/a
14	CUX1	chr3:109646225-109646317	GM12878	blood:	n/a	n/a
15	E2F4	chr3:109644022-109644330	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr3:109646091-109646316	MCF10A-Er-Src	breast:	n/a	n/a
17	EBF1	chr3:109646115-109646401	GM12878	blood:	n/a	n/a
18	EBF1	chr3:109642281-109642731	GM12878	blood:	n/a	n/a
19	EBF1	chr3:109646001-109646522	GM12878	blood:	n/a	n/a
20	EP300	chr3:109645303-109646716	SK-N-SH	brain:	n/a	chr3:109646247-109646256
21	EP300	chr3:109641470-109642274	SK-N-SH	brain:	n/a	chr3:109641598-109641612 chr3:109641602-109641611 chr3:109641856-109641870 chr3:109641861-109641875
22	EP300	chr3:109645786-109646644	ECC-1	luminal epithelium:	n/a	chr3:109646247-109646256
23	EP300	chr3:109645793-109646386	SK-N-SH_RA	brain:	n/a	chr3:109646247-109646256
24	EP300	chr3:109640393-109640719	SK-N-SH_RA	brain:	n/a	n/a
25	EP300	chr3:109645840-109646399	SK-N-SH_RA	brain:	n/a	chr3:109646247-109646256
26	EP300	chr3:109645792-109646601	A549	lung:	n/a	chr3:109646247-109646256
27	EP300	chr3:109639586-109639934	SK-N-SH_RA	brain:	n/a	n/a
28	EP300	chr3:109645925-109646468	Hela-S3	cervix:	n/a	chr3:109646247-109646256
29	EP300	chr3:109645649-109646647	SK-N-SH	brain:	n/a	chr3:109646247-109646256
30	EP300	chr3:109645704-109646664	A549	lung:	n/a	chr3:109646247-109646256
31	EP300	chr3:109639364-109640177	SK-N-SH	brain:	n/a	n/a
32	EP300	chr3:109645914-109646461	ECC-1	luminal epithelium:	n/a	chr3:109646247-109646256
33	FOS	chr3:109645956-109646446	MCF10A-Er-Src	breast:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646246-109646257 chr3:109646247-109646257
34	FOS	chr3:109645991-109646469	MCF10A-Er-Src	breast:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646246-109646257 chr3:109646247-109646257
35	FOS	chr3:109642765-109642963	MCF10A-Er-Src	breast:	n/a	chr3:109642802-109642813 chr3:109642799-109642810 chr3:109642800-109642809
36	FOS	chr3:109645590-109646554	MCF10A-Er-Src	breast:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646246-109646257 chr3:109646247-109646257
37	FOS	chr3:109642793-109642981	MCF10A-Er-Src	breast:	n/a	chr3:109642802-109642813 chr3:109642799-109642810 chr3:109642800-109642809
38	FOS	chr3:109646072-109646414	HUVEC	blood vessel:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646246-109646257 chr3:109646247-109646257
39	FOS	chr3:109646042-109646409	Hela-S3	cervix:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646246-109646257 chr3:109646247-109646257
40	FOS	chr3:109645932-109646725	MCF10A-Er-Src	breast:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646246-109646257 chr3:109646247-109646257
41	FOSL1	chr3:109645858-109646601	HCT-116	colon:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646247-109646257
42	FOSL1	chr3:109645178-109647014	HCT-116	colon:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646247-109646257
43	FOSL2	chr3:109645948-109646447	A549	lung:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646247-109646257
44	FOSL2	chr3:109645875-109646541	SK-N-SH	brain:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646247-109646257
45	FOSL2	chr3:109645893-109646593	SK-N-SH	brain:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646247-109646257
46	FOSL2	chr3:109645675-109646614	A549	lung:	n/a	chr3:109646247-109646257 chr3:109646248-109646257 chr3:109646247-109646257
47	FOXA2	chr3:109645991-109646362	A549	lung:	n/a	n/a
48	FOXM1	chr3:109645890-109646652	ECC-1	luminal epithelium:	n/a	n/a
49	FOXM1	chr3:109645605-109646690	SK-N-SH	brain:	n/a	n/a
50	GABPA	chr3:109645880-109646426	A549	lung:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:109645423-109645473	ProgFib	skin:	n/a
2	chr3:109645423-109645473	HRCEpiC	kidney:	n/a
3	chr3:109645423-109645473	SKMC	muscle:	n/a
4	chr3:109645423-109645473	U87	brain:	n/a
5	chr3:109645423-109645473	HCF	heart:	n/a
6	chr3:109645423-109645473	CMK	blood:	n/a
7	chr3:109645423-109645473	Hepatocyte	liver:	n/a
8	chr3:109645423-109645473	HAEpiC	amniotic membrane:	n/a
9	chr3:109645423-109645473	MCF10A-Er-Src	breast:	n/a
10	chr3:109645423-109645473	SAEC	small airway:	n/a
11	chr3:109645423-109645473	AG04450	lung:	fetal
12	chr3:109645423-109645473	NHDF-neo	bronchial:	n/a
13	chr3:109645423-109645473	HIPEpiC	eye:	n/a
14	chr3:109645423-109645473	AG04449	skin:	fetal
15	chr3:109645423-109645473	HNPCEpiC	eye:	n/a
16	chr3:109645423-109645473	HRE	kidney:	n/a
17	chr3:109645423-109645473	ECC-1	luminal epithelium:	n/a
18	chr3:109645423-109645473	SK-N-MC	brain:	n/a
19	chr3:109645423-109645473	HUVEC	blood vessel:	n/a
20	chr3:109645423-109645473	HRPEpiC	eye:	n/a
21	chr3:109645423-109645473	GM19239	blood:	n/a
22	chr3:109645423-109645473	HCPEpiC	choroid plexus:	n/a
23	chr3:109645423-109645473	AoSMC	blood vessel:	n/a
24	chr3:109645423-109645473	HEEpiC	esophagus:	n/a
25	chr3:109645423-109645473	HCT-116	colon:	n/a
26	chr3:109645423-109645473	NH-A	brain:	n/a
27	chr3:109645423-109645473	H1-hESC	embryonic stem cell:	embryo
28	chr3:109645423-109645473	HepG2	liver:	n/a
29	chr3:109645423-109645473	HCM	heart:	n/a
30	chr3:109645423-109645473	AG09319	gingival:	n/a
31	chr3:109645423-109645473	HMEC	breast:	n/a
32	chr3:109645423-109645473	T-47D	breast:	n/a
33	chr3:109645423-109645473	BJ	skin:	n/a
34	chr3:109645423-109645473	NT2-D1	testis:	n/a
35	chr3:109645423-109645473	Caco-2	colon:	n/a
36	chr3:109645423-109645473	MCF-7	breast:	n/a
37	chr3:109645423-109645473	GM12892	blood:	n/a
38	chr3:109645423-109645473	LNCaP	prostate:	n/a
39	chr3:109645423-109645473	A549	lung:	n/a
40	chr3:109645423-109645473	K562	blood:	n/a
41	chr3:109645423-109645473	PrEC	prostate:	n/a
42	chr3:109645423-109645473	IMR90	lung:	fetal
43	chr3:109645423-109645473	NB4	blood:	n/a
44	chr3:109645423-109645473	HL-60	blood:	n/a
45	chr3:109645423-109645473	ovcar-3	ovarian:	n/a
46	chr3:109645423-109645473	NHBE	bronchial:	n/a
47	chr3:109645423-109645473	GM12878	blood:	n/a
48	chr3:109645423-109645473	HPAEpiC	pulmonary alveolar:	n/a
49	chr3:109645423-109645473	RPTEC	kidney:	n/a
50	chr3:109645423-109645473	SK-N-SH	brain:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:109641317..109642258-chr6:152662604..152663366,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214380	TF binding region
ENSG00000214380	CpG island

Extended variants
information (count: 339 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:339 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs201689981	chr3:109638554-109638555	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs207463509	chr3:109638624-109638625	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs185020052	chr3:109638650-109638651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs573999437	chr3:109638689-109638690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs542177473	chr3:109638700-109638701	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs62283088	chr3:109638714-109638715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs77560780	chr3:109638720-109638721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs189396830	chr3:109638727-109638728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs565075009	chr3:109638728-109638729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs142948193	chr3:109638758-109638759	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs541312510	chr3:109638760-109638761	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs147717137	chr3:109638784-109638785	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs543853069	chr3:109638795-109638796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs530023159	chr3:109638862-109638863	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs549372748	chr3:109638896-109638897	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs6803300	chr3:109638904-109638905	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs531827843	chr3:109638967-109638968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs551627373	chr3:109639007-109639008	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs571809383	chr3:109639011-109639012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs534086545	chr3:109639021-109639022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs375998868	chr3:109639028-109639029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs75270851	chr3:109639056-109639057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs181044030	chr3:109639071-109639072	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs536568902	chr3:109639088-109639089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs555717473	chr3:109639103-109639104	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs575666321	chr3:109639109-109639110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs34073167	chr3:109639130-109639131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs6803668	chr3:109639134-109639135	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs138846316	chr3:109639156-109639157	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs35133826	chr3:109639234-109639235	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs558413370	chr3:109639235-109639236	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs146962807	chr3:109639251-109639252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs652762	chr3:109639259-109639260	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs185931110	chr3:109639329-109639330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs115367976	chr3:109639387-109639388	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs137976584	chr3:109639529-109639530	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs529928633	chr3:109639540-109639541	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs543776933	chr3:109639588-109639589	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs562863918	chr3:109639665-109639666	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs73217646	chr3:109639718-109639719	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs115787118	chr3:109639752-109639753	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs563257441	chr3:109639810-109639811	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs565194569	chr3:109639812-109639813	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs530399602	chr3:109639825-109639826	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs11926268	chr3:109639847-109639848	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs547646668	chr3:109639901-109639902	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs544220467	chr3:109639922-109639923	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs536531709	chr3:109639936-109639937	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs374584585	chr3:109639957-109639958	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs140718092	chr3:109640016-109640017	Enhancers Weak transcription	TF binding region	1 gene(s)	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
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
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	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
Renal cell carcinoma	18765545	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Multiple myeloma	17550852	CNVD
Ductal carcinoma	22052326	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:109630000-109642400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:109637400-109645200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:109637800-109640600	Weak transcription	A549	lung
4	chr3:109639800-109641000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:109640000-109640800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:109640400-109640600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:109640400-109640600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:109640400-109640800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:109640400-109640800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:109640400-109640800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:109640400-109640800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:109640600-109641000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:109640600-109641400	Enhancers	Fetal Lung	lung
14	chr3:109640600-109641600	Enhancers	Dnd41	blood
15	chr3:109640600-109641800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:109640600-109644400	Enhancers	A549	lung
17	chr3:109640800-109641200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:109640800-109642400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:109640800-109646000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:109641000-109641600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:109641000-109645200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:109641200-109641600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:109641200-109643600	Enhancers	Hela-S3	cervix
24	chr3:109641400-109641600	Enhancers	HSMM	muscle
25	chr3:109641400-109642400	Weak transcription	Fetal Lung	lung
26	chr3:109641600-109641800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:109641600-109644200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:109641600-109646600	Weak transcription	HSMM	muscle
29	chr3:109641800-109642000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:109642000-109642600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:109642000-109643000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:109642000-109643400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:109642400-109642600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:109642400-109643000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:109642400-109643000	Enhancers	Fetal Lung	lung
36	chr3:109642400-109643200	Enhancers	HMEC	breast
37	chr3:109642400-109644200	Enhancers	NHEK	skin
38	chr3:109642600-109644400	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr3:109642800-109643200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:109643000-109645200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:109643000-109646800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:109643200-109644400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr3:109643200-109644400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr3:109643200-109645200	Weak transcription	HMEC	breast
45	chr3:109643400-109643800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:109643400-109645400	Enhancers	Placenta	Placenta
47	chr3:109643600-109644000	Weak transcription	Hela-S3	cervix
48	chr3:109643600-109644200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:109643800-109644000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:109644000-109644200	Enhancers	Hela-S3	cervix

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