Variant report

Variant	nsv873888
Chromosome Location	chr2:39508830-39573521
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:279)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:279 , 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	ARID3A	chr2:39565636-39565931	K562	blood:	n/a	n/a
2	CCNT2	chr2:39525801-39525966	K562	blood:	n/a	n/a
3	CEBPB	chr2:39531927-39532215	K562	blood:	n/a	n/a
4	CEBPB	chr2:39531907-39532278	MCF-7	breast:	n/a	n/a
5	CEBPB	chr2:39523389-39523635	IMR90	lung:	n/a	n/a
6	CEBPB	chr2:39531887-39532429	HepG2	liver:	n/a	n/a
7	CEBPB	chr2:39536641-39536800	K562	blood:	n/a	n/a
8	CEBPB	chr2:39531899-39532359	A549	lung:	n/a	n/a
9	CEBPB	chr2:39565527-39565883	K562	blood:	n/a	n/a
10	CEBPB	chr2:39540873-39541107	IMR90	lung:	n/a	n/a
11	CEBPB	chr2:39567618-39567844	A549	lung:	n/a	chr2:39567784-39567795
12	CEBPB	chr2:39536643-39536825	A549	lung:	n/a	n/a
13	CEBPB	chr2:39567654-39567912	HepG2	liver:	n/a	chr2:39567784-39567795
14	CEBPB	chr2:39531884-39532253	Hela-S3	cervix:	n/a	n/a
15	CEBPB	chr2:39523390-39523652	HepG2	liver:	n/a	n/a
16	CEBPB	chr2:39536610-39536879	IMR90	lung:	n/a	n/a
17	CEBPB	chr2:39531891-39532296	IMR90	lung:	n/a	n/a
18	CEBPD	chr2:39565641-39566115	K562	blood:	n/a	n/a
19	CEBPD	chr2:39565590-39566071	K562	blood:	n/a	n/a
20	CTCF	chr2:39553880-39554030	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr2:39513386-39513486	ProgFib	skin:	n/a	n/a
22	CTCF	chr2:39509144-39509225	Medullo	brain:	n/a	n/a
23	CTCF	chr2:39553860-39554010	HEK293	kidney:	n/a	n/a
24	CTCF	chr2:39553880-39554030	HFF-Myc	foreskin:	n/a	n/a
25	CTCF	chr2:39553908-39554079	MCF-7	breast:	n/a	n/a
26	CTCF	chr2:39553920-39554070	HBMEC	blood vessel:	n/a	n/a
27	CTCF	chr2:39553900-39554050	MCF-7	breast:	n/a	n/a
28	CTCF	chr2:39554080-39554230	A549	lung:	n/a	n/a
29	CTCF	chr2:39564980-39565130	SK-N-SH_RA	brain:	n/a	n/a
30	CTCF	chr2:39553880-39554030	MCF-7	breast:	n/a	n/a
31	CTCF	chr2:39553945-39554050	MCF-7	breast:	n/a	n/a
32	CTCF	chr2:39553960-39554110	GM12872	blood:	n/a	n/a
33	CTCF	chr2:39553887-39554086	MCF-7	breast:	n/a	n/a
34	CTCF	chr2:39513395-39513490	MCF-7	breast:	n/a	n/a
35	CTCF	chr2:39553900-39554050	BJ	skin:	n/a	n/a
36	CTCF	chr2:39513404-39513466	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr2:39553860-39554010	BE2_C	brain:	n/a	n/a
38	CTCF	chr2:39553910-39554058	MCF-7	breast:	n/a	n/a
39	CTCF	chr2:39553880-39554030	HRPEpiC	eye:	n/a	n/a
40	CTCF	chr2:39553880-39554030	NHEK	skin:	n/a	n/a
41	CTCF	chr2:39553940-39554090	HCPEpiC	choroid plexus:	n/a	n/a
42	CTCF	chr2:39553946-39553996	K562	blood:	n/a	n/a
43	CTCF	chr2:39553960-39554110	HCT-116	colon:	n/a	n/a
44	CTCF	chr2:39553880-39554030	HepG2	liver:	n/a	n/a
45	CTCF	chr2:39553860-39554010	HCPEpiC	choroid plexus:	n/a	n/a
46	CTCF	chr2:39553920-39554070	HPF	lung:	n/a	n/a
47	CTCF	chr2:39553840-39553990	RPTEC	kidney:	n/a	n/a
48	CTCF	chr2:39553972-39554028	MCF-7	breast:	n/a	n/a
49	CTCF	chr2:39553860-39554010	WERI-Rb-1	eye:	n/a	n/a
50	CTCF	chr2:39553880-39554030	GM12871	blood:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39548716..39551632-chr2:39563065..39564786,2	MCF-7	breast:
2	chr2:39558231..39561041-chr2:39565339..39568222,3	MCF-7	breast:
3	chr2:39564092..39565886-chr2:39568968..39572461,3	K562	blood:
4	chr2:39531304..39535719-chr2:39536825..39539603,4	K562	blood:
5	chr2:39554923..39556541-chr2:39556726..39558880,2	MCF-7	breast:
6	chr2:39539961..39541586-chr2:39667193..39669640,2	K562	blood:
7	chr2:39531304..39535719-chr2:39536825..39539603,4	K562	blood:
8	chr2:39556941..39559571-chr2:39560724..39563297,3	K562	blood:
9	chr2:39558231..39561041-chr2:39565339..39568222,3	MCF-7	breast:
10	chr2:39554819..39557461-chr2:39561282..39564126,2	K562	blood:
11	chr2:39524953..39527718-chr4:1713296..1715250,2	MCF-7	breast:
12	chr2:39508670..39510493-chr2:39518099..39520672,2	K562	blood:
13	chr2:39554923..39556541-chr2:39556726..39558880,2	MCF-7	breast:
14	chr2:39566705..39571966-chr2:39574367..39577562,4	K562	blood:
15	chr2:39556058..39558190-chr2:39561076..39562731,2	MCF-7	breast:
16	chr2:39540552..39542645-chr2:39544069..39547445,3	K562	blood:
17	chr2:39556058..39558190-chr2:39561076..39562731,2	MCF-7	breast:
18	chr2:39564092..39565886-chr2:39568968..39572461,3	K562	blood:
19	chr2:39498139..39500783-chr2:39514401..39516226,2	K562	blood:
20	chr2:39569119..39570627-chr2:39583431..39586281,2	K562	blood:
21	chr2:39508670..39510493-chr2:39518099..39520672,2	K562	blood:
22	chr2:39540552..39542645-chr2:39544069..39547445,3	K562	blood:
23	chr2:39554819..39557461-chr2:39561282..39564126,2	K562	blood:
24	chr2:39556941..39559571-chr2:39560724..39563297,3	K562	blood:
25	chr2:39560253..39562366-chr2:39574869..39577046,2	K562	blood:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDKL4-3	chr2:39511169-39511421	expReg_chr2_3022_-
2	lnc-TMEM178-4	chr2:39555172-39558253	l_1814_chr2:39518006-39558253_76bGuttman_hLF
3	lnc-CDKL4-6	chr2:39550469-39550945	ENSG00000273035.1
4	lnc-TMEM178-4	chr2:39518007-39518182	l_1814_chr2:39518006-39558253_76bGuttman_hLF
5	lnc-TMEM178-4	chr2:39534484-39534610	l_1814_chr2:39518006-39558253_76bGuttman_hLF
6	lnc-TMEM178-4	chr2:39534902-39535010	l_1814_chr2:39518006-39558253_76bGuttman_hLF

No data

Variant related genes	Relation type
MAP4K3	TF binding region
ENSG00000273035	TF binding region
ENSG00000252473	TF binding region
ENSG00000273035	chromatin interactions
ENSG00000270195	chromatin interactions
ENSG00000163950	chromatin interactions

Extended variants
information (count: 2695 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:2695 , 50 per page) page: 1 2 3 4 5 6 7 ... 54

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17023573	chr2:39508830-39508831	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs531015445	chr2:39508851-39508852	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs554523417	chr2:39508853-39508854	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs375079947	chr2:39508891-39508892	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs111256893	chr2:39508900-39508901	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs60025924	chr2:39508936-39508937	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs542048568	chr2:39508995-39508996	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs151162111	chr2:39509019-39509020	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs573391077	chr2:39509028-39509029	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs540599021	chr2:39509064-39509065	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs112846494	chr2:39509100-39509101	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs532830990	chr2:39509147-39509148	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs550951131	chr2:39509160-39509161	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs576060878	chr2:39509228-39509229	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs181943023	chr2:39509242-39509243	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs530200855	chr2:39509273-39509274	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs548388617	chr2:39509279-39509280	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs184131655	chr2:39509284-39509285	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs189453519	chr2:39509303-39509304	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs552149590	chr2:39509317-39509318	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs58168334	chr2:39509350-39509351	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs570395239	chr2:39509354-39509355	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs60938752	chr2:39509357-39509358	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs6725790	chr2:39509363-39509364	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs574806712	chr2:39509375-39509376	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs535610940	chr2:39509409-39509410	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs554036404	chr2:39509413-39509414	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs373345700	chr2:39509436-39509437	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs573370024	chr2:39509531-39509532	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs540412536	chr2:39509537-39509538	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs577267782	chr2:39509542-39509543	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs115220249	chr2:39509551-39509552	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs375102576	chr2:39509574-39509575	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs544613423	chr2:39509579-39509580	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs75489393	chr2:39509601-39509602	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs530359011	chr2:39509606-39509607	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs377630237	chr2:39509607-39509608	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs181042876	chr2:39509628-39509629	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs560363486	chr2:39509629-39509630	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs371079705	chr2:39509646-39509647	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs150038225	chr2:39509654-39509655	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs78142399	chr2:39509689-39509690	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs199706884	chr2:39509710-39509711	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs368082867	chr2:39509711-39509712	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs537416357	chr2:39509733-39509734	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs371197498	chr2:39509736-39509737	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs370622491	chr2:39509749-39509750	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs549820379	chr2:39509755-39509756	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs568347928	chr2:39509776-39509777	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs17506209	chr2:39509841-39509842	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:61)

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
Breast cancer	22522925	CNVD
T-cell lymphomas	22341440	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:1277 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39473400-39517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:39476600-39527600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:39478600-39543400	Weak transcription	Stomach Mucosa	stomach
4	chr2:39479000-39521200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:39481000-39580200	Weak transcription	NHEK	skin
6	chr2:39484400-39516400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:39487600-39513200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:39493600-39523800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:39493600-39565800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:39493800-39509800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr2:39493800-39516600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:39493800-39525000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:39494000-39525600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:39494000-39553000	Weak transcription	GM12878-XiMat	blood
15	chr2:39495600-39510400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:39495600-39523200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:39496400-39521200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:39496600-39515000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:39496600-39520400	Strong transcription	Placenta	Placenta
20	chr2:39497000-39510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:39497000-39516600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:39497200-39516000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:39503400-39511200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:39504000-39511400	Weak transcription	Primary B cells from cord blood	blood
25	chr2:39504400-39521400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:39504600-39510200	Weak transcription	A549	lung
27	chr2:39504600-39512200	Weak transcription	NHLF	lung
28	chr2:39504600-39513000	Weak transcription	Colonic Mucosa	Colon
29	chr2:39504600-39513200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:39504600-39513200	Weak transcription	Fetal Brain Female	brain
31	chr2:39504600-39513200	Weak transcription	Gastric	stomach
32	chr2:39504600-39513200	Weak transcription	Pancreas	Pancrea
33	chr2:39504600-39515000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:39504600-39523600	Weak transcription	Brain Substantia Nigra	brain
35	chr2:39504600-39540000	Weak transcription	Right Ventricle	heart
36	chr2:39504600-39562000	Weak transcription	Psoas Muscle	Psoas
37	chr2:39504800-39509600	Weak transcription	Fetal Heart	heart
38	chr2:39504800-39510000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:39504800-39510200	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:39504800-39511400	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr2:39504800-39512400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:39504800-39512800	Weak transcription	HUVEC	blood vessel
43	chr2:39504800-39513200	Weak transcription	Brain Anterior Caudate	brain
44	chr2:39504800-39513200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:39504800-39513200	Weak transcription	HMEC	breast
46	chr2:39504800-39518400	Weak transcription	Esophagus	oesophagus
47	chr2:39504800-39518800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:39504800-39521800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:39504800-39527800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:39504800-39538400	Weak transcription	Small Intestine	intestine

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