Variant report

Variant	esv1810552
Chromosome Location	chr3:98337517-98379709
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:284)
CpG islands
(count:610)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:284 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr3:98361493-98361992	GM12878	blood:	n/a	n/a
2	BCL3	chr3:98363038-98363376	GM12878	blood:	n/a	n/a
3	BCLAF1	chr3:98376201-98376680	GM12878	blood:	n/a	chr3:98376421-98376434 chr3:98376499-98376512 chr3:98376513-98376526 chr3:98376506-98376519 chr3:98376426-98376435
4	BHLHE40	chr3:98376356-98376616	K562	blood:	n/a	chr3:98376427-98376443
5	BHLHE40	chr3:98376344-98376584	GM12878	blood:	n/a	chr3:98376427-98376443
6	CEBPB	chr3:98338564-98338840	HepG2	liver:	n/a	n/a
7	CEBPB	chr3:98338574-98338890	A549	lung:	n/a	n/a
8	CEBPB	chr3:98369822-98369921	A549	lung:	n/a	n/a
9	CEBPB	chr3:98376488-98376509	H1-hESC	embryonic stem cell:	n/a	n/a
10	CHD2	chr3:98376413-98376532	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:98376460-98376610	GM12864	blood:	n/a	n/a
12	CTCF	chr3:98376329-98376626	GM19239	blood:	n/a	n/a
13	CTCF	chr3:98376400-98376590	GM10248	blood:	n/a	n/a
14	CTCF	chr3:98363520-98363670	MCF-7	breast:	n/a	n/a
15	CTCF	chr3:98376420-98376570	GM12866	blood:	n/a	n/a
16	CTCF	chr3:98376437-98376519	HepG2	liver:	n/a	n/a
17	CTCF	chr3:98376321-98376628	GM19240	blood:	n/a	n/a
18	CTCF	chr3:98376383-98376587	Medullo	brain:	n/a	n/a
19	CTCF	chr3:98376440-98376590	AG04450	lung:	n/a	n/a
20	CTCF	chr3:98376386-98376601	GM13977	blood:	n/a	n/a
21	CTCF	chr3:98376380-98376530	HUVEC	blood vessel:	n/a	n/a
22	CTCF	chr3:98376380-98376530	RPTEC	kidney:	n/a	n/a
23	CTCF	chr3:98376460-98376610	HMF	breast:	n/a	n/a
24	CTCF	chr3:98376426-98376566	K562	blood:	n/a	n/a
25	CTCF	chr3:98376342-98376623	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr3:98348921-98349018	GM13976	blood:	n/a	n/a
27	CTCF	chr3:98376400-98376550	GM12865	blood:	n/a	n/a
28	CTCF	chr3:98363540-98363690	GM12873	blood:	n/a	n/a
29	CTCF	chr3:98376420-98376570	HCT-116	colon:	n/a	n/a
30	CTCF	chr3:98376460-98376610	GM12873	blood:	n/a	n/a
31	CTCF	chr3:98376376-98376582	Kidney_OC	kidney:	n/a	n/a
32	CTCF	chr3:98376347-98376620	A549	lung:	n/a	n/a
33	CTCF	chr3:98376438-98376562	GM20000	blood:	n/a	n/a
34	CTCF	chr3:98376400-98376550	GM12873	blood:	n/a	n/a
35	CTCF	chr3:98376344-98376624	GM12892	blood:	n/a	n/a
36	CTCF	chr3:98376440-98376590	HMF	breast:	n/a	n/a
37	CTCF	chr3:98376334-98376638	GM19238	blood:	n/a	n/a
38	CTCF	chr3:98376219-98376622	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr3:98376399-98376568	A549	lung:	n/a	n/a
40	CTCF	chr3:98376247-98376573	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr3:98376360-98376510	BE2_C	brain:	n/a	n/a
42	CTCF	chr3:98376420-98376570	HPF	lung:	n/a	n/a
43	CTCF	chr3:98376380-98376530	Caco-2	colon:	n/a	n/a
44	CTCF	chr3:98376400-98376550	HRPEpiC	eye:	n/a	n/a
45	CTCF	chr3:98376380-98376530	GM12874	blood:	n/a	n/a
46	CTCF	chr3:98376333-98376623	NHEK	skin:	n/a	n/a
47	CTCF	chr3:98378860-98379010	HRPEpiC	eye:	n/a	n/a
48	CTCF	chr3:98376302-98376627	K562	blood:	n/a	n/a
49	CTCF	chr3:98376440-98376590	HUVEC	blood vessel:	n/a	n/a
50	CTCF	chr3:98376226-98376849	A549	lung:	n/a	n/a

(count:610 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:98342807-98342857	GM12878	blood:	n/a
2	chr3:98376029-98376079	HEEpiC	esophagus:	n/a
3	chr3:98376938-98376988	Hepatocyte	liver:	n/a
4	chr3:98376478-98376528	A549	lung:	n/a
5	chr3:98376427-98376477	LNCaP	prostate:	n/a
6	chr3:98376427-98376477	HCT-116	colon:	n/a
7	chr3:98372781-98372831	HRE	kidney:	n/a
8	chr3:98376574-98376624	LNCaP	prostate:	n/a
9	chr3:98376029-98376079	SK-N-SH_RA	brain:	n/a
10	chr3:98376427-98376477	HAEpiC	amniotic membrane:	n/a
11	chr3:98376390-98376440	HCF	heart:	n/a
12	chr3:98376478-98376528	NHDF-neo	bronchial:	n/a
13	chr3:98376029-98376079	MCF10A-Er-Src	breast:	n/a
14	chr3:98342807-98342857	HEK293	kidney:	embryo
15	chr3:98376574-98376624	SK-N-SH	brain:	n/a
16	chr3:98372781-98372831	HEK293	kidney:	embryo
17	chr3:98379208-98379258	HRCEpiC	kidney:	n/a
18	chr3:98376427-98376477	H1-hESC	embryonic stem cell:	embryo
19	chr3:98379208-98379258	NT2-D1	testis:	n/a
20	chr3:98376029-98376079	AG10803	skin:	n/a
21	chr3:98376478-98376528	HRCEpiC	kidney:	n/a
22	chr3:98376390-98376440	Jurkat	blood:	n/a
23	chr3:98376478-98376528	AG09309	skin:	n/a
24	chr3:98376390-98376440	HEEpiC	esophagus:	n/a
25	chr3:98343882-98343932	HNPCEpiC	eye:	n/a
26	chr3:98342807-98342857	PrEC	prostate:	n/a
27	chr3:98343882-98343932	GM12878	blood:	n/a
28	chr3:98342807-98342857	HAEpiC	amniotic membrane:	n/a
29	chr3:98343882-98343932	LNCaP	prostate:	n/a
30	chr3:98376029-98376079	ProgFib	skin:	n/a
31	chr3:98376478-98376528	AG10803	skin:	n/a
32	chr3:98342807-98342857	NH-A	brain:	n/a
33	chr3:98376390-98376440	PrEC	prostate:	n/a
34	chr3:98343882-98343932	HepG2	liver:	n/a
35	chr3:98376574-98376624	SK-N-MC	brain:	n/a
36	chr3:98376478-98376528	ECC-1	luminal epithelium:	n/a
37	chr3:98376390-98376440	GM19239	blood:	n/a
38	chr3:98376574-98376624	HCM	heart:	n/a
39	chr3:98343882-98343932	BE2_C	brain:	n/a
40	chr3:98376938-98376988	NT2-D1	testis:	n/a
41	chr3:98376478-98376528	HMEC	breast:	n/a
42	chr3:98379208-98379258	AG04449	skin:	fetal
43	chr3:98376938-98376988	AoSMC	blood vessel:	n/a
44	chr3:98376574-98376624	HRE	kidney:	n/a
45	chr3:98376427-98376477	HEK293	kidney:	embryo
46	chr3:98376478-98376528	T-47D	breast:	n/a
47	chr3:98376574-98376624	RPTEC	kidney:	n/a
48	chr3:98343882-98343932	NHDF-neo	bronchial:	n/a
49	chr3:98376938-98376988	A549	lung:	n/a
50	chr3:98376427-98376477	ECC-1	luminal epithelium:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52332749..52333464-chr3:98352060..98352684,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR15-2	chr3:98338909-98339462	NONHSAT090806
2	lnc-ST3GAL6-5	chr3:98376584-98377010	NONHSAT090808

No data

Variant related genes	Relation type
ENSG00000266233	TF binding region
WWP1P1	TF binding region
ENSG00000240827	TF binding region
ENSG00000266233	CpG island
WWP1P1	CpG island
ENSG00000240827	CpG island

Extended variants
information (count: 1217 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:1217 , 50 per page) page: 1 2 3 4 5 6 7 ... 25

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7630058	chr3:98337517-98337518	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs145352311	chr3:98337518-98337519	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs143887111	chr3:98338544-98338545	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs185399063	chr3:98338561-98338562	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs562197930	chr3:98338563-98338564	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs549616490	chr3:98338588-98338589	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs138009008	chr3:98338589-98338590	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs11926174	chr3:98338595-98338596	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs375727595	chr3:98338596-98338597	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs547972128	chr3:98338615-98338616	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs527694286	chr3:98338630-98338631	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs189929545	chr3:98338700-98338701	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs570632946	chr3:98338711-98338712	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs148186166	chr3:98338712-98338713	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs549606155	chr3:98338718-98338719	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs569830831	chr3:98338765-98338766	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs535249860	chr3:98338773-98338774	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs193044402	chr3:98338791-98338792	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs531286244	chr3:98338794-98338795	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs144109866	chr3:98338818-98338819	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs78452155	chr3:98338823-98338824	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs56315640	chr3:98338828-98338829	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs557767071	chr3:98338843-98338844	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs577845425	chr3:98338847-98338848	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs74338717	chr3:98338858-98338859	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs543532255	chr3:98338878-98338879	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs185635745	chr3:98338911-98338912	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs112422659	chr3:98338982-98338983	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs542016363	chr3:98338992-98338993	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs562419936	chr3:98339084-98339085	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs527950686	chr3:98339103-98339104	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs547413927	chr3:98339110-98339111	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs564131333	chr3:98339131-98339132	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs114155495	chr3:98339135-98339136	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs190441855	chr3:98339139-98339140	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs13086863	chr3:98339244-98339245	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs376833465	chr3:98339251-98339252	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs13087002	chr3:98339267-98339268	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs570013570	chr3:98339276-98339277	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs7647570	chr3:98339277-98339278	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs527835993	chr3:98339286-98339287	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs180908939	chr3:98339328-98339329	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs557826278	chr3:98339367-98339368	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs548581103	chr3:98339411-98339412	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs77975109	chr3:98339414-98339415	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs536995635	chr3:98339434-98339435	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs557024949	chr3:98339446-98339447	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs575360278	chr3:98341863-98341864	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs140788686	chr3:98341889-98341890	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs561048913	chr3:98341899-98341900	Enhancers	n/a	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
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:177 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98335400-98337600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:98335600-98337600	Enhancers	Brain Hippocampus Middle	brain
3	chr3:98341800-98343200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:98341800-98343600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:98342000-98343600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:98342000-98343600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:98342000-98343800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:98342000-98343800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:98342200-98342800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr3:98342400-98343800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:98342600-98343200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr3:98342600-98343400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:98343400-98345000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:98343600-98347200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:98345000-98345400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:98347200-98347400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:98349600-98350400	Enhancers	Fetal Intestine Small	intestine
18	chr3:98349600-98351000	Enhancers	Fetal Intestine Large	intestine
19	chr3:98357200-98358400	Active TSS	Liver	Liver
20	chr3:98358400-98360200	Weak transcription	Liver	Liver
21	chr3:98360200-98361000	Enhancers	Liver	Liver
22	chr3:98360400-98360600	Enhancers	Fetal Intestine Small	intestine
23	chr3:98360400-98361200	ZNF genes & repeats	GM12878-XiMat	blood
24	chr3:98360600-98361200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:98361200-98361400	Enhancers	Fetal Intestine Small	intestine
26	chr3:98361200-98361600	Flanking Active TSS	GM12878-XiMat	blood
27	chr3:98361600-98363000	Enhancers	GM12878-XiMat	blood
28	chr3:98362200-98363800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:98362400-98363200	Enhancers	Dnd41	blood
30	chr3:98363000-98364400	ZNF genes & repeats	GM12878-XiMat	blood
31	chr3:98363200-98363400	Flanking Active TSS	Dnd41	blood
32	chr3:98363200-98366400	Enhancers	Fetal Thymus	thymus
33	chr3:98363400-98363600	Enhancers	Dnd41	blood
34	chr3:98363400-98363800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:98363400-98364200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:98363400-98364200	Enhancers	Esophagus	oesophagus
37	chr3:98363600-98363800	Flanking Active TSS	Dnd41	blood
38	chr3:98363600-98364400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:98363600-98364400	Enhancers	NHEK	skin
40	chr3:98363600-98366400	Enhancers	Thymus	Thymus
41	chr3:98363800-98364200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr3:98363800-98364200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:98363800-98364200	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr3:98363800-98364200	Enhancers	HepG2	liver
45	chr3:98363800-98364200	Enhancers	HMEC	breast
46	chr3:98363800-98364400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:98363800-98364400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:98363800-98364400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:98363800-98364400	Enhancers	Placenta	Placenta
50	chr3:98363800-98364400	Enhancers	Right Ventricle	heart

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