Variant report

Variant	nsv963233
Chromosome Location	chr2:54278282-54280313
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:212)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:212 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr2:54280074-54280274	K562	blood:	n/a	n/a
2	CHD1	chr2:54279554-54279633	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr2:54279883-54279959	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr2:54280080-54280230	HPAF	blood vessel:	n/a	n/a
5	CTCF	chr2:54280120-54280270	AG10803	skin:	n/a	n/a
6	CTCF	chr2:54280120-54280270	HEEpiC	esophagus:	n/a	n/a
7	CTCF	chr2:54280080-54280230	GM12868	blood:	n/a	n/a
8	CTCF	chr2:54279800-54279950	NHDF-neo	bronchial:	n/a	chr2:54279821-54279830
9	CTCF	chr2:54280156-54280262	GM12892	blood:	n/a	n/a
10	CTCF	chr2:54280130-54280269	Fibrobl	skin:	n/a	n/a
11	CTCF	chr2:54279720-54279870	HCT-116	colon:	n/a	chr2:54279821-54279830
12	CTCF	chr2:54280074-54280252	ProgFib	skin:	n/a	n/a
13	CTCF	chr2:54280080-54280230	HFF-Myc	foreskin:	n/a	n/a
14	CTCF	chr2:54280080-54280230	GM12801	blood:	n/a	n/a
15	CTCF	chr2:54280100-54280250	HepG2	liver:	n/a	n/a
16	CTCF	chr2:54279780-54279930	GM12873	blood:	n/a	chr2:54279821-54279830
17	CTCF	chr2:54280020-54280170	BE2_C	brain:	n/a	n/a
18	CTCF	chr2:54280120-54280270	GM12871	blood:	n/a	n/a
19	CTCF	chr2:54280060-54280210	GM12870	blood:	n/a	n/a
20	CTCF	chr2:54279720-54279870	GM12875	blood:	n/a	chr2:54279821-54279830
21	CTCF	chr2:54279700-54279850	AG10803	skin:	n/a	chr2:54279821-54279830
22	CTCF	chr2:54279570-54280435	HCT-116	colon:	n/a	chr2:54279821-54279830
23	CTCF	chr2:54280080-54280230	K562	blood:	n/a	n/a
24	CTCF	chr2:54280049-54280274	GM12878	blood:	n/a	n/a
25	CTCF	chr2:54280120-54280270	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr2:54280060-54280210	HCM	heart:	n/a	n/a
27	CTCF	chr2:54280040-54280190	HFF-Myc	foreskin:	n/a	n/a
28	CTCF	chr2:54280095-54280247	HepG2	liver:	n/a	n/a
29	CTCF	chr2:54279720-54279870	AoAF	blood vessel:	n/a	chr2:54279821-54279830
30	CTCF	chr2:54280060-54280210	AG10803	skin:	n/a	n/a
31	CTCF	chr2:54280060-54280210	HCT-116	colon:	n/a	n/a
32	CTCF	chr2:54280120-54280270	HA-sp	spinal cord:	n/a	n/a
33	CTCF	chr2:54280080-54280230	HCPEpiC	choroid plexus:	n/a	n/a
34	CTCF	chr2:54280080-54280230	HCT-116	colon:	n/a	n/a
35	CTCF	chr2:54280100-54280250	AG04450	lung:	n/a	n/a
36	CTCF	chr2:54280100-54280250	GM12875	blood:	n/a	n/a
37	CTCF	chr2:54280180-54280330	NHLF	lung:	n/a	n/a
38	CTCF	chr2:54279760-54279910	MCF-7	breast:	n/a	chr2:54279821-54279830
39	CTCF	chr2:54280120-54280270	AG04450	lung:	n/a	n/a
40	CTCF	chr2:54279680-54279830	HA-sp	spinal cord:	n/a	chr2:54279821-54279830
41	CTCF	chr2:54280080-54280230	GM12865	blood:	n/a	n/a
42	CTCF	chr2:54279660-54279810	HCM	heart:	n/a	n/a
43	CTCF	chr2:54280060-54280210	AG09319	gingival:	n/a	n/a
44	CTCF	chr2:54279760-54279910	Caco-2	colon:	n/a	chr2:54279821-54279830
45	CTCF	chr2:54280100-54280250	NHEK	skin:	n/a	n/a
46	CTCF	chr2:54280100-54280250	GM12867	blood:	n/a	n/a
47	CTCF	chr2:54280120-54280270	NHEK	skin:	n/a	n/a
48	CTCF	chr2:54280080-54280230	WERI-Rb-1	eye:	n/a	n/a
49	CTCF	chr2:54279740-54279890	GM12865	blood:	n/a	chr2:54279821-54279830
50	CTCF	chr2:54279840-54279990	HFF	foreskin:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54196526..54198487-chr2:54280269..54283258,2	MCF-7	breast:
2	chr2:54279730..54280237-chr2:54311516..54312403,2	MCF-7	breast:
3	chr2:54279392..54279928-chr2:54311498..54312280,2	MCF-7	breast:
4	chr2:54196632..54198799-chr2:54280134..54282598,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSME4-2	chr2:54279531-54279583	NONHSAT070719
2	lnc-PSME4-2	chr2:54279456-54279477	NONHSAT070719
3	lnc-ACYP2-3	chr2:54278471-54278897	NONHSAT070725
4	lnc-PSME4-2	chr2:54278721-54279184	NONHSAT070719
5	lnc-PSME4-2	chr2:54279631-54279665	NONHSAT070719
6	lnc-PSME4-2	chr2:54279610-54279622	NONHSAT070719

No data

Variant related genes	Relation type
HMGB1P31	TF binding region
ENSG00000170634	chromatin interactions
ENSG00000068878	chromatin interactions

Extended variants
information (count: 93 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:93 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536738008	chr2:54278294-54278295	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs558787916	chr2:54278298-54278299	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs58694216	chr2:54278358-54278359	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs150036134	chr2:54278370-54278371	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs58333745	chr2:54278395-54278396	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs567509194	chr2:54278430-54278431	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs373494581	chr2:54278455-54278456	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs145490228	chr2:54278462-54278463	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs569954973	chr2:54278472-54278473	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs570091985	chr2:54278485-54278486	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs186426736	chr2:54278528-54278529	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs7576901	chr2:54278533-54278534	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs1974771	chr2:54278543-54278544	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs541164467	chr2:54278556-54278557	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs530129062	chr2:54278567-54278568	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs190835898	chr2:54278573-54278574	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs375503628	chr2:54278579-54278580	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs1559037	chr2:54278585-54278586	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs7590819	chr2:54278604-54278605	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs77620080	chr2:54278619-54278620	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs546158983	chr2:54278625-54278626	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs182986453	chr2:54278631-54278632	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs10192559	chr2:54278639-54278640	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs528467475	chr2:54278645-54278646	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs7590846	chr2:54278667-54278668	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs531817663	chr2:54278672-54278673	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs560408331	chr2:54278681-54278682	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs530997504	chr2:54278742-54278743	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs550016143	chr2:54278772-54278773	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs569733938	chr2:54278804-54278805	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs538950536	chr2:54278823-54278824	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs148860266	chr2:54278861-54278862	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs528714562	chr2:54278896-54278897	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs34576311	chr2:54278909-54278910	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs550060022	chr2:54278931-54278932	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs565280206	chr2:54278932-54278933	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs143442872	chr2:54278933-54278934	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs140645362	chr2:54278935-54278936	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs574211957	chr2:54278947-54278948	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs536735785	chr2:54278995-54278996	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs141979743	chr2:54279044-54279045	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs187253239	chr2:54279052-54279053	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs371337101	chr2:54279078-54279079	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs146104119	chr2:54279118-54279119	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs567416492	chr2:54279139-54279140	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs375576851	chr2:54279162-54279163	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs190136401	chr2:54279165-54279166	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs201160349	chr2:54279183-54279184	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs568848741	chr2:54279184-54279185	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs58161337	chr2:54279212-54279213	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
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
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	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
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54248600-54289800	Weak transcription	Fetal Lung	lung
2	chr2:54266200-54281800	Weak transcription	Fetal Intestine Large	intestine
3	chr2:54268200-54282400	Weak transcription	Right Ventricle	heart
4	chr2:54268400-54286800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:54268400-54290800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:54270400-54280200	Weak transcription	Ovary	ovary
7	chr2:54271400-54286800	Weak transcription	HSMMtube	muscle
8	chr2:54271800-54281600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:54272000-54280200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:54272000-54280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:54272000-54286600	Weak transcription	HSMM	muscle
12	chr2:54272200-54281600	Weak transcription	Brain Angular Gyrus	brain
13	chr2:54272200-54282800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:54272600-54279800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:54272600-54280000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:54272600-54280000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:54272600-54280000	Weak transcription	Brain Substantia Nigra	brain
18	chr2:54272600-54280000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:54272600-54280400	Weak transcription	Brain Germinal Matrix	brain
20	chr2:54272600-54286600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:54272600-54286800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:54273000-54278400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:54273000-54292400	Weak transcription	Fetal Brain Female	brain
24	chr2:54274800-54280600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:54275200-54279800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:54275800-54279800	Weak transcription	Osteobl	bone
27	chr2:54275800-54280000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:54275800-54280200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:54276000-54278400	Weak transcription	Primary T cells from cord blood	blood
30	chr2:54276000-54279600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:54276000-54280000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:54276000-54280200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:54276200-54278400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:54276200-54279800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:54276200-54280000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:54276200-54280000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:54276200-54280200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:54276200-54280200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:54276200-54280200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:54276200-54280200	Weak transcription	HMEC	breast
41	chr2:54276200-54280400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:54276200-54280400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:54276200-54280400	Weak transcription	K562	blood
44	chr2:54276200-54281600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:54276200-54281600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:54276600-54280200	Weak transcription	Lung	lung
47	chr2:54276800-54279800	Weak transcription	Brain Anterior Caudate	brain
48	chr2:54276800-54280600	Weak transcription	Esophagus	oesophagus
49	chr2:54276800-54281000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:54276800-54286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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