Variant report

Variant	esv2756698
Chromosome Location	chr3:89642587-89732392
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	ARID3A	chr3:89673701-89674049	HepG2	liver:	n/a	n/a
2	BATF	chr3:89681279-89681512	GM12878	blood:	n/a	n/a
3	CEBPB	chr3:89677575-89677724	A549	lung:	n/a	chr3:89677682-89677695
4	CEBPB	chr3:89684505-89684527	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr3:89688131-89688356	HepG2	liver:	n/a	chr3:89688223-89688234
6	CEBPB	chr3:89673160-89673467	HepG2	liver:	n/a	chr3:89673310-89673321 chr3:89673312-89673323 chr3:89673310-89673323 chr3:89673310-89673323
7	CEBPB	chr3:89710509-89710837	HepG2	liver:	n/a	chr3:89710668-89710679
8	CEBPB	chr3:89684395-89684690	Hela-S3	cervix:	n/a	n/a
9	CEBPB	chr3:89684350-89684696	IMR90	lung:	n/a	n/a
10	CEBPB	chr3:89671217-89671525	HepG2	liver:	n/a	chr3:89671346-89671357
11	CEBPB	chr3:89688146-89688365	IMR90	lung:	n/a	chr3:89688223-89688234
12	CEBPB	chr3:89728923-89729158	HepG2	liver:	n/a	n/a
13	CTCF	chr3:89705927-89705987	GM20000	blood:	n/a	n/a
14	CTCF	chr3:89666920-89667070	AG09319	gingival:	n/a	n/a
15	CTCF	chr3:89697461-89697546	GM13976	blood:	n/a	n/a
16	CTCF	chr3:89698420-89698570	GM12864	blood:	n/a	n/a
17	CTCF	chr3:89661505-89661561	Medullo	brain:	n/a	n/a
18	E2F4	chr3:89675260-89675349	MCF10A-Er-Src	breast:	n/a	n/a
19	E2F4	chr3:89670746-89671021	MCF10A-Er-Src	breast:	n/a	n/a
20	E2F4	chr3:89654899-89655009	MCF10A-Er-Src	breast:	n/a	n/a
21	E2F4	chr3:89682163-89682216	MCF10A-Er-Src	breast:	n/a	n/a
22	E2F4	chr3:89643789-89643921	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F4	chr3:89698697-89698885	MCF10A-Er-Src	breast:	n/a	n/a
24	EBF1	chr3:89711993-89712296	GM12878	blood:	n/a	chr3:89712125-89712136
25	EP300	chr3:89673646-89674019	HepG2	liver:	n/a	n/a
26	FAM48A	chr3:89724560-89724613	GM12878	blood:	n/a	n/a
27	FOS	chr3:89690216-89690530	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr3:89655475-89655496	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr3:89684401-89684635	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr3:89690230-89690474	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr3:89684403-89684631	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr3:89698734-89698800	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr3:89690232-89690504	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr3:89655454-89655504	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr3:89655306-89655628	MCF10A-Er-Src	breast:	n/a	n/a
36	FOXA1	chr3:89673688-89673967	HepG2	liver:	n/a	n/a
37	FOXA1	chr3:89675088-89675428	HepG2	liver:	n/a	n/a
38	FOXA1	chr3:89673616-89674027	HepG2	liver:	n/a	n/a
39	FOXA1	chr3:89673680-89673969	HepG2	liver:	n/a	n/a
40	FOXA1	chr3:89673579-89673995	HepG2	liver:	n/a	n/a
41	FOXA2	chr3:89675143-89675352	HepG2	liver:	n/a	n/a
42	FOXA2	chr3:89673724-89674001	HepG2	liver:	n/a	n/a
43	GATA3	chr3:89676875-89677075	SH-SY5Y	brain:	n/a	n/a
44	JUN	chr3:89728947-89729151	HepG2	liver:	n/a	chr3:89729044-89729057
45	JUN	chr3:89644923-89644966	H1-hESC	embryonic stem cell:	n/a	n/a
46	JUN	chr3:89662682-89662684	H1-hESC	embryonic stem cell:	n/a	n/a
47	JUND	chr3:89728892-89729215	HepG2	liver:	n/a	n/a
48	KAP1	chr3:89705371-89706042	HEK293	kidney:	n/a	n/a
49	MAFF	chr3:89664795-89664925	HepG2	liver:	n/a	n/a
50	MAFF	chr3:89646345-89646533	HepG2	liver:	n/a	chr3:89646454-89646472

No.	Distal block	Cell Line	Cell type
1	chr3:89648727..89651109-chr3:89653242..89655047,2	MCF-7	breast:
2	chr3:89648727..89651109-chr3:89653242..89655047,2	MCF-7	breast:
3	chr2:127952533..127953285-chr3:89714580..89715363,2	MCF-7	breast:
4	chr3:89645876..89647847-chr3:89649873..89652502,3	MCF-7	breast:
5	chr1:11968828..11971360-chr3:89649996..89651496,2	K562	blood:
6	chr20:52424950..52427553-chr3:89710194..89711857,2	MCF-7	breast:
7	chr3:89645876..89647847-chr3:89649873..89652502,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240951	TF binding region
ENSG00000240309	TF binding region
ENSG00000201801	chromatin interactions

Extended variants
information (count: 1163 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:1163 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6780506	chr3:89642587-89642588	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs138685837	chr3:89642600-89642601	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs141146070	chr3:89642602-89642603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs555512165	chr3:89642613-89642614	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs184291583	chr3:89642668-89642669	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs150313803	chr3:89642695-89642696	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
7	rs188720551	chr3:89642743-89642744	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs567102315	chr3:89642802-89642803	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs192865900	chr3:89642833-89642834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs552765008	chr3:89642878-89642879	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs184482666	chr3:89642906-89642907	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs538729025	chr3:89642932-89642933	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs140871007	chr3:89642948-89642949	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs72925633	chr3:89642979-89642980	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs137986424	chr3:89643012-89643013	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs575773089	chr3:89643014-89643015	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs544542937	chr3:89643068-89643069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs562939598	chr3:89643080-89643081	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs562393731	chr3:89643106-89643107	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs574405902	chr3:89643115-89643116	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs58835418	chr3:89643138-89643139	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs551762053	chr3:89643157-89643158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs559995608	chr3:89643171-89643172	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs533265859	chr3:89643192-89643193	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs149390860	chr3:89643210-89643211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs367807631	chr3:89643238-89643239	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs189314108	chr3:89643330-89643331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs182207606	chr3:89643340-89643341	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs187200735	chr3:89643370-89643371	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs548989140	chr3:89643391-89643392	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs189109965	chr3:89643443-89643444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs181752223	chr3:89643450-89643451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs144810703	chr3:89643451-89643452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs546341380	chr3:89643497-89643498	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs571155406	chr3:89643509-89643510	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs538345400	chr3:89643542-89643543	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs557052763	chr3:89643553-89643554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs186011048	chr3:89643573-89643574	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs190385573	chr3:89643574-89643575	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs115463823	chr3:89643622-89643623	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs6801632	chr3:89643650-89643651	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs541795103	chr3:89643807-89643808	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs546464708	chr3:89643813-89643814	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs370870256	chr3:89643814-89643815	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs6810037	chr3:89643817-89643818	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs77742014	chr3:89643826-89643827	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs563775566	chr3:89643831-89643832	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs530926693	chr3:89643887-89643888	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs542573461	chr3:89643952-89643953	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs560951527	chr3:89643967-89643968	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:71)

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
Acute lymphoblastic leukemia	20435627	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
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89637200-89650600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:89652400-89652800	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr3:89662400-89662600	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr3:89662400-89662800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:89662400-89662800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:89662400-89662800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:89662400-89662800	Enhancers	Ovary	ovary
8	chr3:89662400-89663800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:89662800-89663600	Weak transcription	Ovary	ovary
10	chr3:89663600-89663800	Enhancers	Ovary	ovary
11	chr3:89663800-89664800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:89663800-89666800	Weak transcription	Ovary	ovary
13	chr3:89664800-89665200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:89665200-89674600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:89666800-89667200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:89666800-89667600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:89666800-89667600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:89666800-89667600	Bivalent Enhancer	Fetal Heart	heart
19	chr3:89666800-89667600	Enhancers	HMEC	breast
20	chr3:89667000-89667200	Enhancers	Ovary	ovary
21	chr3:89667000-89667400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:89673600-89673800	Enhancers	HepG2	liver
23	chr3:89674000-89675000	Weak transcription	HepG2	liver
24	chr3:89674600-89675200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:89675000-89675400	Enhancers	HepG2	liver
26	chr3:89675200-89675600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:89675600-89675800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:89677600-89679000	Enhancers	Fetal Heart	heart
29	chr3:89678200-89678800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:89702000-89702400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:89702400-89703000	Enhancers	Aorta	Aorta
32	chr3:89707400-89707600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:89707800-89708200	Enhancers	Colon Smooth Muscle	Colon
34	chr3:89710200-89711200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:89710600-89711000	Enhancers	Adipose Nuclei	Adipose
36	chr3:89712400-89712800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:89724800-89725400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:89725400-89726400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:89726400-89727000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:89731200-89732200	Enhancers	HUES48 Cell Line	embryonic stem cell

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