Variant report

Variant	esv3407132
Chromosome Location	chr4:3678704-3681502
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:3679639-3679806	HepG2	liver:	n/a	n/a
2	CTCF	chr4:3679340-3679550	A549	lung:	n/a	n/a
3	CTCF	chr4:3679480-3679630	WERI-Rb-1	eye:	n/a	n/a
4	CTCF	chr4:3679460-3679610	HepG2	liver:	n/a	n/a
5	CTCF	chr4:3679460-3679610	HCT-116	colon:	n/a	n/a
6	CTCF	chr4:3679420-3679570	HEK293	kidney:	n/a	n/a
7	CTCF	chr4:3679485-3679621	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr4:3679469-3679558	HepG2	liver:	n/a	n/a
9	CTCF	chr4:3679316-3679632	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr4:3679540-3679690	WERI-Rb-1	eye:	n/a	n/a
11	CTCF	chr4:3679380-3679530	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr4:3679420-3679570	BE2_C	brain:	n/a	n/a
13	CTCF	chr4:3679460-3679610	GM12873	blood:	n/a	n/a
14	CTCF	chr4:3679505-3679566	Gliobla	brain:	n/a	n/a
15	CTCF	chr4:3679440-3679590	HCT-116	colon:	n/a	n/a
16	CTCF	chr4:3679478-3679584	MCF-7	breast:	n/a	n/a
17	CTCF	chr4:3680104-3680138	GM10266	blood:	n/a	n/a
18	E2F4	chr4:3679042-3679126	MCF10A-Er-Src	breast:	n/a	n/a
19	RAD21	chr4:3679268-3679732	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr4:3679425-3679630	HepG2	liver:	n/a	n/a
21	SPI1	chr4:3681017-3681444	HL-60	blood:	n/a	chr4:3681229-3681238 chr4:3681227-3681240
22	SPI1	chr4:3681082-3681322	HL-60	blood:	n/a	chr4:3681229-3681238 chr4:3681227-3681240
23	SPI1	chr4:3681102-3681278	K562	blood:	n/a	chr4:3681229-3681238 chr4:3681227-3681240
24	ZNF263	chr4:3679716-3680706	HEK293-T-REx	kidney:	n/a	chr4:3680460-3680481 chr4:3680408-3680429

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3680721-3680771	Caco-2	colon:	n/a
2	chr4:3680970-3681020	HCT-116	colon:	n/a
3	chr4:3680970-3681020	AG09319	gingival:	n/a
4	chr4:3680721-3680771	HIPEpiC	eye:	n/a
5	chr4:3680721-3680771	SK-N-MC	brain:	n/a
6	chr4:3680721-3680771	HL-60	blood:	n/a
7	chr4:3680721-3680771	BJ	skin:	n/a
8	chr4:3680721-3680771	CMK	blood:	n/a
9	chr4:3680721-3680771	Hela-S3	cervix:	n/a
10	chr4:3680721-3680771	SK-N-SH	brain:	n/a
11	chr4:3680970-3681020	NHDF-neo	bronchial:	n/a
12	chr4:3680721-3680771	HMEC	breast:	n/a
13	chr4:3680970-3681020	Hepatocyte	liver:	n/a
14	chr4:3680970-3681020	T-47D	breast:	n/a
15	chr4:3680970-3681020	Jurkat	blood:	n/a
16	chr4:3680970-3681020	Hela-S3	cervix:	n/a
17	chr4:3680970-3681020	AG09309	skin:	n/a
18	chr4:3680721-3680771	HEK293	kidney:	embryo
19	chr4:3680970-3681020	K562	blood:	n/a
20	chr4:3680721-3680771	ECC-1	luminal epithelium:	n/a
21	chr4:3680721-3680771	AG10803	skin:	n/a
22	chr4:3680970-3681020	A549	lung:	n/a
23	chr4:3680970-3681020	PANC-1	pancreas:	n/a
24	chr4:3680721-3680771	HCF	heart:	n/a
25	chr4:3680721-3680771	ProgFib	skin:	n/a
26	chr4:3680970-3681020	HMEC	breast:	n/a
27	chr4:3680721-3680771	U87	brain:	n/a
28	chr4:3680970-3681020	BJ	skin:	n/a
29	chr4:3680721-3680771	HPAEpiC	pulmonary alveolar:	n/a
30	chr4:3680721-3680771	LNCaP	prostate:	n/a
31	chr4:3680721-3680771	T-47D	breast:	n/a
32	chr4:3680970-3681020	HL-60	blood:	n/a
33	chr4:3680970-3681020	SK-N-SH_RA	brain:	n/a
34	chr4:3680721-3680771	HUVEC	blood vessel:	n/a
35	chr4:3680970-3681020	HepG2	liver:	n/a
36	chr4:3680970-3681020	NT2-D1	testis:	n/a
37	chr4:3680970-3681020	H1-hESC	embryonic stem cell:	embryo
38	chr4:3680721-3680771	HCPEpiC	choroid plexus:	n/a
39	chr4:3680970-3681020	AG10803	skin:	n/a
40	chr4:3680970-3681020	ovcar-3	ovarian:	n/a
41	chr4:3680970-3681020	PFSK-1	brain:	n/a
42	chr4:3680721-3680771	NB4	blood:	n/a
43	chr4:3680970-3681020	GM12892	blood:	n/a
44	chr4:3680721-3680771	GM12878	blood:	n/a
45	chr4:3680970-3681020	NB4	blood:	n/a
46	chr4:3680970-3681020	CMK	blood:	n/a
47	chr4:3680970-3681020	Caco-2	colon:	n/a
48	chr4:3680970-3681020	HCPEpiC	choroid plexus:	n/a
49	chr4:3680970-3681020	GM06990	blood:	n/a
50	chr4:3680721-3680771	BE2_C	brain:	n/a

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRPAP1-2	chr4:3678898-3679582	ENSG00000250632
2	lnc-LRPAP1-2	chr4:3678898-3679582	XLOC_003861

No data

Variant related genes	Relation type
ENSG00000250632	TF binding region
ENSG00000250632	CpG island

Extended variants
information (count: 137 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:137 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs115034697	chr4:3678734-3678735	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs368903602	chr4:3678771-3678772	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs58077843	chr4:3678788-3678789	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs373436896	chr4:3678789-3678790	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs569949552	chr4:3678797-3678798	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs535988298	chr4:3678798-3678799	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs146359953	chr4:3678809-3678810	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs572177145	chr4:3678824-3678825	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs533751172	chr4:3678838-3678839	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs553507694	chr4:3678856-3678857	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs577909412	chr4:3678865-3678866	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs543149962	chr4:3678875-3678876	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs139727472	chr4:3678881-3678882	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs545774236	chr4:3678882-3678883	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs557887148	chr4:3678914-3678915	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
16	rs575931816	chr4:3678950-3678951	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
17	rs541974648	chr4:3678952-3678953	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
18	rs561788735	chr4:3678959-3678960	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
19	rs527348678	chr4:3678961-3678962	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
20	rs541654880	chr4:3678969-3678970	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
21	rs192781917	chr4:3679011-3679012	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs58476965	chr4:3679039-3679040	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs74497205	chr4:3679041-3679042	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs529290505	chr4:3679042-3679043	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs373144432	chr4:3679065-3679066	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs548929779	chr4:3679073-3679074	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs116244585	chr4:3679115-3679116	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs113381807	chr4:3679136-3679137	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs544275253	chr4:3679163-3679164	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs553595519	chr4:3679184-3679185	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs10001474	chr4:3679208-3679209	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs115930152	chr4:3679223-3679224	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
33	rs553342712	chr4:3679239-3679240	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
34	rs574640607	chr4:3679254-3679255	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
35	rs556162201	chr4:3679271-3679272	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
36	rs184914427	chr4:3679299-3679300	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
37	rs542056634	chr4:3679316-3679317	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
38	rs555361642	chr4:3679328-3679329	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
39	rs572175868	chr4:3679329-3679330	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
40	rs377623479	chr4:3679358-3679359	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
41	rs114472420	chr4:3679361-3679362	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
42	rs149639714	chr4:3679377-3679378	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
43	rs187786288	chr4:3679404-3679405	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs59916646	chr4:3679434-3679435	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs192754849	chr4:3679439-3679440	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs6827536	chr4:3679491-3679492	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs58062370	chr4:3679504-3679505	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs563911615	chr4:3679509-3679510	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs567966334	chr4:3679526-3679527	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs528610170	chr4:3679549-3679550	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Lung cancer	18438408	CNVD

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3669400-3693400	Weak transcription	Right Atrium	heart
2	chr4:3674200-3678800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:3678000-3678800	ZNF genes & repeats	Spleen	Spleen
4	chr4:3678000-3679000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:3678000-3679000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr4:3678200-3679400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:3678600-3679000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:3678800-3679400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:3678800-3681800	Weak transcription	Spleen	Spleen
10	chr4:3679000-3679800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:3679000-3680800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:3679200-3679400	Bivalent Enhancer	Fetal Stomach	stomach
13	chr4:3679400-3679600	Enhancers	HSMM	muscle
14	chr4:3679400-3685400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:3679600-3679800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
16	chr4:3680000-3680200	Enhancers	Fetal Kidney	kidney
17	chr4:3680400-3680600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:3680800-3682000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:3680800-3682000	Bivalent Enhancer	Fetal Stomach	stomach
20	chr4:3681000-3682000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr4:3681000-3682000	Enhancers	HSMMtube	muscle
22	chr4:3681200-3681400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr4:3681200-3682000	Bivalent Enhancer	Fetal Muscle Leg	muscle

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