Variant report

Variant	esv2759165
Chromosome Location	chr3:103256253-103421162
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	ATF2	chr3:103290808-103291325	GM12878	blood:	n/a	n/a
2	ATF2	chr3:103290805-103291256	GM12878	blood:	n/a	n/a
3	BATF	chr3:103290849-103291204	GM12878	blood:	n/a	n/a
4	BCL11A	chr3:103290919-103291146	GM12878	blood:	n/a	n/a
5	BHLHE40	chr3:103397888-103397904	GM12878	blood:	n/a	n/a
6	CEBPB	chr3:103308326-103308613	A549	lung:	n/a	n/a
7	CEBPB	chr3:103382914-103383111	K562	blood:	n/a	chr3:103382968-103382979
8	CEBPB	chr3:103409586-103409918	HepG2	liver:	n/a	chr3:103409756-103409767
9	CEBPB	chr3:103308333-103308643	HepG2	liver:	n/a	chr3:103308614-103308625
10	CEBPB	chr3:103293018-103293124	H1-hESC	embryonic stem cell:	n/a	chr3:103293074-103293083
11	CEBPB	chr3:103283597-103283720	HepG2	liver:	n/a	chr3:103283614-103283625
12	CEBPB	chr3:103409583-103409923	IMR90	lung:	n/a	chr3:103409756-103409767
13	CEBPB	chr3:103382804-103383148	HepG2	liver:	n/a	chr3:103382968-103382979
14	CEBPB	chr3:103420562-103420867	HepG2	liver:	n/a	n/a
15	CEBPB	chr3:103382873-103383028	H1-hESC	embryonic stem cell:	n/a	chr3:103382968-103382979
16	CEBPB	chr3:103409595-103409925	Hela-S3	cervix:	n/a	chr3:103409756-103409767
17	CEBPB	chr3:103333974-103334184	Hela-S3	cervix:	n/a	chr3:103334066-103334079
18	CEBPB	chr3:103382777-103383147	Hela-S3	cervix:	n/a	chr3:103382968-103382979
19	CEBPB	chr3:103409629-103409911	H1-hESC	embryonic stem cell:	n/a	chr3:103409756-103409767
20	CEBPB	chr3:103308326-103308617	IMR90	lung:	n/a	n/a
21	CEBPB	chr3:103409661-103409927	A549	lung:	n/a	chr3:103409756-103409767
22	CEBPB	chr3:103333518-103334035	ECC-1	luminal epithelium:	n/a	n/a
23	CEBPB	chr3:103409600-103409927	MCF-7	breast:	n/a	chr3:103409756-103409767
24	CEBPB	chr3:103372844-103373261	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr3:103382798-103383151	IMR90	lung:	n/a	chr3:103382968-103382979
26	CEBPB	chr3:103333586-103334020	ECC-1	luminal epithelium:	n/a	n/a
27	CREB1	chr3:103290886-103291258	GM12878	blood:	n/a	n/a
28	CREB1	chr3:103290847-103291325	GM12878	blood:	n/a	n/a
29	CTCF	chr3:103328371-103328696	MCF-7	breast:	n/a	n/a
30	CTCF	chr3:103398740-103398890	SK-N-SH_RA	brain:	n/a	chr3:103398772-103398790 chr3:103398774-103398795
31	CTCF	chr3:103328411-103328613	MCF-7	breast:	n/a	n/a
32	CTCF	chr3:103321644-103321702	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:103328421-103328606	LNCaP	prostate:	n/a	n/a
34	CTCF	chr3:103398680-103398830	MCF-7	breast:	n/a	chr3:103398772-103398790 chr3:103398774-103398795
35	CTCF	chr3:103331920-103332070	BE2_C	brain:	n/a	n/a
36	CTCF	chr3:103328440-103328590	HMEC	breast:	n/a	n/a
37	CTCF	chr3:103385480-103385630	NHEK	skin:	n/a	n/a
38	CTCF	chr3:103328425-103328627	Medullo	brain:	n/a	n/a
39	CTCF	chr3:103347840-103347990	HEEpiC	esophagus:	n/a	n/a
40	CTCF	chr3:103328436-103328600	MCF-7	breast:	n/a	n/a
41	CTCF	chr3:103316895-103316978	GM13976	blood:	n/a	n/a
42	CTCF	chr3:103375636-103375718	ProgFib	skin:	n/a	n/a
43	CTCF	chr3:103385480-103385630	HBMEC	blood vessel:	n/a	n/a
44	CTCF	chr3:103328440-103328590	AG04449	skin:	n/a	n/a
45	CTCF	chr3:103321500-103321650	RPTEC	kidney:	n/a	n/a
46	CTCF	chr3:103328460-103328610	MCF-7	breast:	n/a	n/a
47	CTCF	chr3:103328433-103328559	Fibrobl	skin:	n/a	n/a
48	CTCF	chr3:103328420-103328570	HMEC	breast:	n/a	n/a
49	CTCF	chr3:103386060-103386210	HRPEpiC	eye:	n/a	n/a
50	CTCF	chr3:103331980-103332130	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:103014701..103015436-chr3:103328029..103328722,3	MCF-7	breast:
2	chr3:103418196..103420246-chr3:103431375..103433647,2	MCF-7	breast:
3	chr3:103014881..103015501-chr3:103328255..103328854,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZPLD1-10	chr3:103366208-103366374	l_2421_chr3:103365266-103366374_testes
2	lnc-ZPLD1-10	chr3:103365267-103365509	l_2421_chr3:103365266-103366374_testes
3	lnc-RPL24-6	chr3:103257479-103259331	NONHSAT090942
4	lnc-ZPLD1-9	chr3:103349505-103349756	NONHSAT090943

Variant related genes	Relation type
TUBBP11	TF binding region
ENSG00000240107	TF binding region

Extended variants
information (count: 2126 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:2126 , 50 per page) page: 1 2 3 4 5 6 7 ... 43

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs528360248	chr3:103257528-103257529	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs79313235	chr3:103257534-103257535	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs536554927	chr3:103257557-103257558	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs148561826	chr3:103257563-103257564	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs567696597	chr3:103257580-103257581	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs11924723	chr3:103257604-103257605	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs546925606	chr3:103257625-103257626	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs578129409	chr3:103257643-103257644	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs566031908	chr3:103257645-103257646	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs62274371	chr3:103257687-103257688	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs545493071	chr3:103257723-103257724	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs186766491	chr3:103257735-103257736	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs572507476	chr3:103257767-103257768	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs114438178	chr3:103257796-103257797	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs372398419	chr3:103257828-103257829	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs561421825	chr3:103257833-103257834	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs531378618	chr3:103257863-103257864	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs201238980	chr3:103257888-103257889	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs573771101	chr3:103257924-103257925	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs369681211	chr3:103257930-103257931	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs532092489	chr3:103257968-103257969	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs144912828	chr3:103258001-103258002	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs191145766	chr3:103258022-103258023	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs180970695	chr3:103258194-103258195	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs369136089	chr3:103258209-103258210	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs536643417	chr3:103258214-103258215	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs369061526	chr3:103258240-103258241	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs184998632	chr3:103258263-103258264	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs569833718	chr3:103258314-103258315	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs538268425	chr3:103258418-103258419	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs556618593	chr3:103258440-103258441	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs189610102	chr3:103258491-103258492	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs376657514	chr3:103258492-103258493	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs554262622	chr3:103258505-103258506	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs372794003	chr3:103258517-103258518	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs542845040	chr3:103258561-103258562	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs555279067	chr3:103258592-103258593	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs77368291	chr3:103258676-103258677	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs543672812	chr3:103258683-103258684	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs369459448	chr3:103258706-103258707	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs564549029	chr3:103258723-103258724	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs140679843	chr3:103258764-103258765	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs554704453	chr3:103258779-103258780	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs562156931	chr3:103258788-103258789	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs559172160	chr3:103258799-103258800	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs77076120	chr3:103258800-103258801	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs74514105	chr3:103258830-103258831	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs138421447	chr3:103258947-103258948	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs77785305	chr3:103258950-103258951	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
50	rs183327462	chr3:103259013-103259014	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
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
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
small cell lung cancer	20016488	CNVD
Ductal carcinoma	22052326	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Myelofibrosis	22110671	CNVD
Renal cell carcinoma	18765545	CNVD
Breast cancer	21364760	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD
Developmental delay	22180640	CNVD

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:103272800-103274200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr3:103273000-103273400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:103273200-103273600	Enhancers	Fetal Lung	lung
4	chr3:103273200-103273800	Active TSS	Fetal Kidney	kidney
5	chr3:103273200-103274000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:103273200-103274000	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:103273200-103274000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:103273200-103274200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:103273200-103274600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:103273400-103274000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:103273600-103274000	Active TSS	Fetal Lung	lung
12	chr3:103273800-103274200	Enhancers	Fetal Kidney	kidney
13	chr3:103282800-103285000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:103328400-103336200	Weak transcription	Pancreas	Pancrea
15	chr3:103333200-103334000	Enhancers	Fetal Lung	lung
16	chr3:103334800-103335000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:103336400-103337800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:103337000-103337800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:103338000-103338600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:103341200-103343600	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:103341400-103342800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:103341600-103344000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:103342800-103343400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:103342800-103343600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:103343400-103344000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:103349600-103349800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:103368200-103368400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:103373600-103375800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr3:103374400-103375400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:103383600-103383800	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr3:103383800-103395000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:103388200-103388600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:103391400-103391800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:103393400-103393800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:103393600-103393800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:103393800-103409000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:103403200-103404000	Enhancers	Fetal Lung	lung
38	chr3:103403800-103404200	Enhancers	Fetal Kidney	kidney
39	chr3:103404200-103404600	Enhancers	Fetal Heart	heart
40	chr3:103409000-103410200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:103412600-103413200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:103412600-103413200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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