Variant report

Variant	esv3342104
Chromosome Location	chr3:20286997-20322223
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:148)
CpG islands
(count:62)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:148 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr3:20288074-20288600	GM12878	blood:	n/a	n/a
2	ATF2	chr3:20288131-20288515	GM12878	blood:	n/a	n/a
3	BATF	chr3:20288183-20288438	GM12878	blood:	n/a	chr3:20288290-20288301
4	BATF	chr3:20288158-20288422	GM12878	blood:	n/a	chr3:20288290-20288301
5	BCL11A	chr3:20288193-20288461	GM12878	blood:	n/a	n/a
6	BCL11A	chr3:20288232-20288418	GM12878	blood:	n/a	n/a
7	BHLHE40	chr3:20306641-20306956	K562	blood:	n/a	n/a
8	CEBPB	chr3:20287304-20287598	MCF-7	breast:	n/a	n/a
9	CEBPB	chr3:20298924-20299012	K562	blood:	n/a	chr3:20298947-20298958
10	CEBPB	chr3:20298810-20299031	HepG2	liver:	n/a	chr3:20298947-20298958
11	CTCF	chr3:20287440-20287590	HRE	kidney:	n/a	n/a
12	CTCF	chr3:20287400-20287550	Caco-2	colon:	n/a	n/a
13	CTCF	chr3:20287380-20287530	HMEC	breast:	n/a	n/a
14	CTCF	chr3:20287397-20287528	Gliobla	brain:	n/a	n/a
15	CTCF	chr3:20287460-20287610	HEEpiC	esophagus:	n/a	n/a
16	CTCF	chr3:20287420-20287570	HCFaa	heart:	n/a	n/a
17	CTCF	chr3:20287340-20287490	SAEC	small airway:	n/a	n/a
18	CTCF	chr3:20287354-20287559	MCF-7	breast:	n/a	n/a
19	CTCF	chr3:20287460-20287610	GM12875	blood:	n/a	n/a
20	CTCF	chr3:20287398-20287464	Lung_OC	lung:	n/a	n/a
21	CTCF	chr3:20287380-20287530	GM12874	blood:	n/a	n/a
22	CTCF	chr3:20287368-20287576	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr3:20287380-20287530	GM12866	blood:	n/a	n/a
24	CTCF	chr3:20287360-20287510	HMF	breast:	n/a	n/a
25	CTCF	chr3:20287440-20287590	HCT-116	colon:	n/a	n/a
26	CTCF	chr3:20287320-20287470	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr3:20287360-20287510	GM06990	blood:	n/a	n/a
28	CTCF	chr3:20287380-20287530	GM12873	blood:	n/a	n/a
29	CTCF	chr3:20287380-20287530	GM12872	blood:	n/a	n/a
30	CTCF	chr3:20287360-20287510	WERI-Rb-1	eye:	n/a	n/a
31	CTCF	chr3:20287360-20287510	HepG2	liver:	n/a	n/a
32	CTCF	chr3:20287340-20287490	GM12872	blood:	n/a	n/a
33	CTCF	chr3:20287360-20287510	GM12865	blood:	n/a	n/a
34	CTCF	chr3:20287400-20287550	SK-N-SH_RA	brain:	n/a	n/a
35	CTCF	chr3:20287420-20287570	GM12864	blood:	n/a	n/a
36	CTCF	chr3:20287420-20287570	HEEpiC	esophagus:	n/a	n/a
37	CTCF	chr3:20287467-20287473	LNCaP	prostate:	n/a	n/a
38	CTCF	chr3:20288240-20288390	HepG2	liver:	n/a	n/a
39	CTCF	chr3:20287420-20287570	GM12871	blood:	n/a	n/a
40	CTCF	chr3:20287380-20287530	NHEK	skin:	n/a	n/a
41	CTCF	chr3:20287320-20287470	WERI-Rb-1	eye:	n/a	n/a
42	CTCF	chr3:20287320-20287470	HCT-116	colon:	n/a	n/a
43	CTCF	chr3:20287400-20287550	GM12873	blood:	n/a	n/a
44	CTCF	chr3:20287400-20287550	GM12871	blood:	n/a	n/a
45	CTCF	chr3:20287400-20287550	HA-sp	spinal cord:	n/a	n/a
46	CTCF	chr3:20287380-20287530	RPTEC	kidney:	n/a	n/a
47	CTCF	chr3:20287340-20287490	HRE	kidney:	n/a	n/a
48	CTCF	chr3:20287420-20287570	RPTEC	kidney:	n/a	n/a
49	CTCF	chr3:20287340-20287723	MCF-7	breast:	n/a	n/a
50	CTCF	chr3:20287347-20287558	K562	blood:	n/a	n/a

(count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:20321584-20321634	HAEpiC	amniotic membrane:	n/a
2	chr3:20321584-20321634	HAEpiC	amniotic membrane:	n/a
3	chr3:20321584-20321634	PANC-1	pancreas:	n/a
4	chr3:20321584-20321634	HL-60	blood:	n/a
5	chr3:20321584-20321634	HCM	heart:	n/a
6	chr3:20321584-20321634	HIPEpiC	eye:	n/a
7	chr3:20321584-20321634	NB4	blood:	n/a
8	chr3:20321584-20321634	AG10803	skin:	n/a
9	chr3:20321584-20321634	CMK	blood:	n/a
10	chr3:20321584-20321634	MCF-7	breast:	n/a
11	chr3:20321584-20321634	HNPCEpiC	eye:	n/a
12	chr3:20321584-20321634	AoSMC	blood vessel:	n/a
13	chr3:20321584-20321634	Hela-S3	cervix:	n/a
14	chr3:20321584-20321634	NT2-D1	testis:	n/a
15	chr3:20321584-20321634	AG09319	gingival:	n/a
16	chr3:20321584-20321634	Caco-2	colon:	n/a
17	chr3:20321584-20321634	HRCEpiC	kidney:	n/a
18	chr3:20321584-20321634	HRE	kidney:	n/a
19	chr3:20321584-20321634	SK-N-SH_RA	brain:	n/a
20	chr3:20321584-20321634	Hepatocyte	liver:	n/a
21	chr3:20321584-20321634	RPTEC	kidney:	n/a
22	chr3:20321584-20321634	PrEC	prostate:	n/a
23	chr3:20321584-20321634	T-47D	breast:	n/a
24	chr3:20321584-20321634	GM12878	blood:	n/a
25	chr3:20321584-20321634	HUVEC	blood vessel:	n/a
26	chr3:20321584-20321634	SK-N-MC	brain:	n/a
27	chr3:20321584-20321634	SK-N-SH	brain:	n/a
28	chr3:20321584-20321634	HCPEpiC	choroid plexus:	n/a
29	chr3:20321584-20321634	HCT-116	colon:	n/a
30	chr3:20321584-20321634	Jurkat	blood:	n/a
31	chr3:20321584-20321634	AG04449	skin:	fetal
32	chr3:20321584-20321634	MCF10A-Er-Src	breast:	n/a
33	chr3:20321584-20321634	NHDF-neo	bronchial:	n/a
34	chr3:20321584-20321634	HMEC	breast:	n/a
35	chr3:20321584-20321634	NHBE	bronchial:	n/a
36	chr3:20321584-20321634	BJ	skin:	n/a
37	chr3:20321584-20321634	HPAEpiC	pulmonary alveolar:	n/a
38	chr3:20321584-20321634	H1-hESC	embryonic stem cell:	embryo
39	chr3:20321584-20321634	SKMC	muscle:	n/a
40	chr3:20321584-20321634	BE2_C	brain:	n/a
41	chr3:20321584-20321634	HEEpiC	esophagus:	n/a
42	chr3:20321584-20321634	GM06990	blood:	n/a
43	chr3:20321584-20321634	GM12891	blood:	n/a
44	chr3:20321584-20321634	IMR90	lung:	fetal
45	chr3:20321584-20321634	AG09309	skin:	n/a
46	chr3:20321584-20321634	ProgFib	skin:	n/a
47	chr3:20321584-20321634	GM12892	blood:	n/a
48	chr3:20321584-20321634	LNCaP	prostate:	n/a
49	chr3:20321584-20321634	ovcar-3	ovarian:	n/a
50	chr3:20321584-20321634	AG04450	lung:	fetal

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

No.	Distal block	Cell Line	Cell type
1	chr3:20316601..20319465-chr3:20319672..20321888,2	K562	blood:
2	chr3:20320265..20323041-chr3:20324824..20326695,2	K562	blood:
3	chr3:20316601..20319465-chr3:20319672..20321888,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KAT2B-6	chr3:20286533-20287951	NONHSAT088619

No data

Variant related genes	Relation type
RNU6-822P	TF binding region
RNU6-822P	CpG island

Extended variants
information (count: 1258 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:1258 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs181095953	chr3:20287016-20287017	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs150151413	chr3:20287070-20287071	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs553514632	chr3:20287102-20287103	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs545786940	chr3:20287135-20287136	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs571978540	chr3:20287137-20287138	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs542526592	chr3:20287147-20287148	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs560807152	chr3:20287221-20287222	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs575831758	chr3:20287259-20287260	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs145563148	chr3:20287278-20287279	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs186763727	chr3:20287296-20287297	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs559995268	chr3:20287309-20287310	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs191552080	chr3:20287310-20287311	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs547843754	chr3:20287332-20287333	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs528737052	chr3:20287342-20287343	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs559505341	chr3:20287366-20287367	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs183803368	chr3:20287382-20287383	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs548783170	chr3:20287394-20287395	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs148864257	chr3:20287400-20287401	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs143502490	chr3:20287427-20287428	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs531222762	chr3:20287431-20287432	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs552837976	chr3:20287446-20287447	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs571001578	chr3:20287453-20287454	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs12638108	chr3:20287463-20287464	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs137917948	chr3:20287478-20287479	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs188693763	chr3:20287513-20287514	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs73818865	chr3:20287517-20287518	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs190787382	chr3:20287540-20287541	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs554139059	chr3:20287551-20287552	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs531036233	chr3:20287553-20287554	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs575969933	chr3:20287565-20287566	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs543293084	chr3:20287592-20287593	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs78880957	chr3:20287649-20287650	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs142372593	chr3:20287750-20287751	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs73818866	chr3:20287755-20287756	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs559752692	chr3:20287783-20287784	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs375477969	chr3:20287789-20287790	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs530216599	chr3:20287807-20287808	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs542285032	chr3:20287812-20287813	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs183272904	chr3:20287835-20287836	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs375934996	chr3:20287863-20287864	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs531258164	chr3:20287911-20287912	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs552808242	chr3:20287925-20287926	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs113836355	chr3:20287942-20287943	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs144590944	chr3:20287968-20287969	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs547176234	chr3:20287973-20287974	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs565812939	chr3:20288002-20288003	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs138494716	chr3:20288031-20288032	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs116188120	chr3:20288089-20288090	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs4858165	chr3:20288151-20288152	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs569283337	chr3:20288158-20288159	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:75)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
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
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Developmental delay	21147756	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20287200-20289000	Enhancers	GM12878-XiMat	blood
2	chr3:20291800-20292200	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr3:20291800-20292400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:20291800-20292400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:20291800-20293400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr3:20291800-20293400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr3:20291800-20293600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:20292000-20292200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:20292000-20293200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr3:20292000-20293200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:20292000-20293200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:20292000-20293200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr3:20292200-20292400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:20292200-20292400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr3:20292200-20292800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:20292200-20293400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:20292200-20293400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:20292400-20292600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:20292400-20292800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr3:20292400-20293200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:20292400-20296000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:20292600-20292800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr3:20292600-20293200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:20292600-20296800	Weak transcription	Ovary	ovary
25	chr3:20292800-20293000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:20292800-20293600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr3:20293000-20293200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:20293200-20293400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:20293400-20295600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:20293400-20295800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:20293600-20295600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:20293600-20297600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:20295600-20296200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:20295600-20296400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr3:20295800-20296000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:20295800-20296200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:20295800-20296200	Active TSS	A549	lung
38	chr3:20295800-20296400	Active TSS	Hela-S3	cervix
39	chr3:20296000-20296600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:20296200-20310800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:20296400-20300400	Enhancers	Hela-S3	cervix
42	chr3:20296600-20306200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:20297000-20299400	Enhancers	HUVEC	blood vessel
44	chr3:20297400-20297600	Enhancers	GM12878-XiMat	blood
45	chr3:20297600-20298000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:20297600-20298000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:20297600-20298000	Flanking Active TSS	GM12878-XiMat	blood
48	chr3:20297600-20298200	Enhancers	NHEK	skin
49	chr3:20297600-20298400	Enhancers	HMEC	breast
50	chr3:20297800-20298000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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