Variant report

Variant	esv2762497
Chromosome Location	chr2:39540753-39566724
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:131)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:131 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr2:39565636-39565931	K562	blood:	n/a	n/a
2	CEBPB	chr2:39565527-39565883	K562	blood:	n/a	n/a
3	CEBPB	chr2:39540873-39541107	IMR90	lung:	n/a	n/a
4	CEBPD	chr2:39565641-39566115	K562	blood:	n/a	n/a
5	CEBPD	chr2:39565590-39566071	K562	blood:	n/a	n/a
6	CTCF	chr2:39553920-39554070	HPF	lung:	n/a	n/a
7	CTCF	chr2:39553946-39553996	K562	blood:	n/a	n/a
8	CTCF	chr2:39553940-39554090	HCPEpiC	choroid plexus:	n/a	n/a
9	CTCF	chr2:39553919-39554044	A549	lung:	n/a	n/a
10	CTCF	chr2:39553840-39553990	RPTEC	kidney:	n/a	n/a
11	CTCF	chr2:39553920-39554070	HBMEC	blood vessel:	n/a	n/a
12	CTCF	chr2:39553860-39554010	WERI-Rb-1	eye:	n/a	n/a
13	CTCF	chr2:39553960-39554110	GM12872	blood:	n/a	n/a
14	CTCF	chr2:39553940-39554090	HPAF	blood vessel:	n/a	n/a
15	CTCF	chr2:39553880-39554030	A549	lung:	n/a	n/a
16	CTCF	chr2:39553920-39554070	BJ	skin:	n/a	n/a
17	CTCF	chr2:39553910-39554058	MCF-7	breast:	n/a	n/a
18	CTCF	chr2:39553880-39554030	GM12871	blood:	n/a	n/a
19	CTCF	chr2:39553908-39554079	MCF-7	breast:	n/a	n/a
20	CTCF	chr2:39554000-39554150	HPAF	blood vessel:	n/a	n/a
21	CTCF	chr2:39553940-39554090	HA-sp	spinal cord:	n/a	n/a
22	CTCF	chr2:39553900-39554050	HMF	breast:	n/a	n/a
23	CTCF	chr2:39553920-39554070	BE2_C	brain:	n/a	n/a
24	CTCF	chr2:39553880-39554030	HRPEpiC	eye:	n/a	n/a
25	CTCF	chr2:39553887-39554086	MCF-7	breast:	n/a	n/a
26	CTCF	chr2:39548843-39548879	Medullo	brain:	n/a	n/a
27	CTCF	chr2:39553880-39554030	HFF-Myc	foreskin:	n/a	n/a
28	CTCF	chr2:39553931-39554055	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr2:39553900-39554050	BJ	skin:	n/a	n/a
30	CTCF	chr2:39553900-39554050	MCF-7	breast:	n/a	n/a
31	CTCF	chr2:39553960-39554110	HCT-116	colon:	n/a	n/a
32	CTCF	chr2:39553972-39554028	MCF-7	breast:	n/a	n/a
33	CTCF	chr2:39553980-39554130	HEEpiC	esophagus:	n/a	n/a
34	CTCF	chr2:39553880-39554030	MCF-7	breast:	n/a	n/a
35	CTCF	chr2:39564980-39565130	SK-N-SH_RA	brain:	n/a	n/a
36	CTCF	chr2:39553945-39554050	MCF-7	breast:	n/a	n/a
37	CTCF	chr2:39553880-39554030	HepG2	liver:	n/a	n/a
38	CTCF	chr2:39553978-39554061	Medullo	brain:	n/a	n/a
39	CTCF	chr2:39553920-39554070	AG04450	lung:	n/a	n/a
40	CTCF	chr2:39554080-39554230	A549	lung:	n/a	n/a
41	CTCF	chr2:39553880-39554030	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr2:39553880-39554030	NHEK	skin:	n/a	n/a
43	CTCF	chr2:39553860-39554010	HEK293	kidney:	n/a	n/a
44	CTCF	chr2:39553860-39554010	HCPEpiC	choroid plexus:	n/a	n/a
45	CTCF	chr2:39553860-39554010	BE2_C	brain:	n/a	n/a
46	CUX1	chr2:39553193-39553276	K562	blood:	n/a	n/a
47	EP300	chr2:39559326-39559415	K562	blood:	n/a	chr2:39559394-39559408
48	EP300	chr2:39565669-39566042	K562	blood:	n/a	n/a
49	EP300	chr2:39542592-39542660	K562	blood:	n/a	n/a
50	FOS	chr2:39540934-39540964	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39558231..39561041-chr2:39565339..39568222,3	MCF-7	breast:
2	chr2:39540552..39542645-chr2:39544069..39547445,3	K562	blood:
3	chr2:39556941..39559571-chr2:39560724..39563297,3	K562	blood:
4	chr2:39548716..39551632-chr2:39563065..39564786,2	MCF-7	breast:
5	chr2:39540552..39542645-chr2:39544069..39547445,3	K562	blood:
6	chr2:39560253..39562366-chr2:39574869..39577046,2	K562	blood:
7	chr2:39554819..39557461-chr2:39561282..39564126,2	K562	blood:
8	chr2:39554923..39556541-chr2:39556726..39558880,2	MCF-7	breast:
9	chr2:39556058..39558190-chr2:39561076..39562731,2	MCF-7	breast:
10	chr2:39554923..39556541-chr2:39556726..39558880,2	MCF-7	breast:
11	chr2:39539961..39541586-chr2:39667193..39669640,2	K562	blood:
12	chr2:39564092..39565886-chr2:39568968..39572461,3	K562	blood:
13	chr2:39566705..39571966-chr2:39574367..39577562,4	K562	blood:
14	chr2:39556941..39559571-chr2:39560724..39563297,3	K562	blood:
15	chr2:39556058..39558190-chr2:39561076..39562731,2	MCF-7	breast:
16	chr2:39558231..39561041-chr2:39565339..39568222,3	MCF-7	breast:
17	chr2:39554819..39557461-chr2:39561282..39564126,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDKL4-6	chr2:39550469-39550945	ENSG00000273035.1
2	lnc-TMEM178-4	chr2:39555172-39558253	l_1814_chr2:39518006-39558253_76bGuttman_hLF

No data

Variant related genes	Relation type
MAP4K3	TF binding region
ENSG00000273035	TF binding region
ENSG00000273035	chromatin interactions

Extended variants
information (count: 1114 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:1114 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200838941	chr2:39540774-39540775	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs549884142	chr2:39540776-39540777	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs568186121	chr2:39540780-39540781	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs11897610	chr2:39540789-39540790	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs553680013	chr2:39540809-39540810	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs370896552	chr2:39540863-39540864	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs368295589	chr2:39540865-39540866	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs575901969	chr2:39540900-39540901	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs111686405	chr2:39540902-39540903	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs557375371	chr2:39540905-39540906	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs149429980	chr2:39540924-39540925	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs144854654	chr2:39540953-39540954	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs539976260	chr2:39540959-39540960	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs575809256	chr2:39540985-39540986	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs372610247	chr2:39541004-39541005	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs11688352	chr2:39541014-39541015	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs34932578	chr2:39541055-39541056	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs556380743	chr2:39541069-39541070	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs574829864	chr2:39541123-39541124	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs541968875	chr2:39541142-39541143	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs76187117	chr2:39541206-39541207	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs572373885	chr2:39541217-39541218	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs181006210	chr2:39541221-39541222	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs564805950	chr2:39541222-39541223	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs186416428	chr2:39541243-39541244	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs113821066	chr2:39541255-39541256	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs550440680	chr2:39541256-39541257	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs575804378	chr2:39541269-39541270	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs368761283	chr2:39541290-39541291	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs189660649	chr2:39541301-39541302	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs528942452	chr2:39541324-39541325	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs372074240	chr2:39541341-39541342	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs546033409	chr2:39541352-39541353	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs565640380	chr2:39541367-39541368	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs374124882	chr2:39541407-39541408	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs181668870	chr2:39541412-39541413	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs185914728	chr2:39541417-39541418	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs148082437	chr2:39541430-39541431	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs536951166	chr2:39541437-39541438	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs190717380	chr2:39541509-39541510	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs141848832	chr2:39541511-39541512	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs147264795	chr2:39541514-39541515	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs6748834	chr2:39541532-39541533	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs572457983	chr2:39541574-39541575	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs183233650	chr2:39541575-39541576	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs75253316	chr2:39541584-39541585	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs544401238	chr2:39541670-39541671	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs564764928	chr2:39541697-39541698	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs34167987	chr2:39541706-39541707	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs576760106	chr2:39541722-39541723	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	21965145	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Neurocytoma	17123091	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16272173	CNVD
T-cell lymphomas	22341440	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:565 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39478600-39543400	Weak transcription	Stomach Mucosa	stomach
2	chr2:39481000-39580200	Weak transcription	NHEK	skin
3	chr2:39493600-39565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:39494000-39553000	Weak transcription	GM12878-XiMat	blood
5	chr2:39504600-39562000	Weak transcription	Psoas Muscle	Psoas
6	chr2:39504800-39541600	Weak transcription	Fetal Brain Male	brain
7	chr2:39504800-39565800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39504800-39567200	Weak transcription	Hela-S3	cervix
9	chr2:39505400-39556800	Weak transcription	Thymus	Thymus
10	chr2:39505400-39557200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:39505400-39562400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:39513600-39555000	Weak transcription	Primary B cells from cord blood	blood
13	chr2:39514400-39541800	Weak transcription	HUVEC	blood vessel
14	chr2:39516200-39557600	Weak transcription	Gastric	stomach
15	chr2:39517200-39552400	Weak transcription	HMEC	breast
16	chr2:39517600-39566400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:39519000-39555200	Weak transcription	Fetal Thymus	thymus
18	chr2:39519800-39553000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:39519800-39555400	Weak transcription	Fetal Heart	heart
20	chr2:39519800-39562200	Weak transcription	K562	blood
21	chr2:39519800-39583000	Weak transcription	Brain Angular Gyrus	brain
22	chr2:39520000-39556600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:39520000-39586200	Weak transcription	Fetal Kidney	kidney
24	chr2:39520200-39553200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:39520200-39555200	Weak transcription	Ovary	ovary
26	chr2:39520400-39565800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr2:39521200-39541000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:39524000-39583600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:39525200-39553400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:39528000-39542000	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:39528200-39551800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr2:39528200-39562800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:39528400-39541800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:39528400-39562800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:39528800-39581800	Weak transcription	Brain Germinal Matrix	brain
36	chr2:39529400-39545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:39531000-39561600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:39532400-39541600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:39533200-39541000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:39533600-39555000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:39534000-39586200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:39534200-39540800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:39534200-39551600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:39534600-39542800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:39535400-39562600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:39535800-39542600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:39536000-39560800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:39536200-39540800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:39536200-39542000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:39537000-39542600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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