Variant report

Variant	nsv1011975
Chromosome Location	chr2:54475866-54495222
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:200)
CpG islands
(count:854)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:200 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr2:54488738-54489020	HepG2	liver:	n/a	n/a
2	ATF1	chr2:54491458-54491517	K562	blood:	n/a	n/a
3	ATF1	chr2:54482380-54482686	K562	blood:	n/a	n/a
4	ATF3	chr2:54482456-54482605	K562	blood:	n/a	n/a
5	BATF	chr2:54486493-54486929	GM12878	blood:	n/a	n/a
6	BATF	chr2:54486550-54486907	GM12878	blood:	n/a	n/a
7	CBX3	chr2:54483260-54483656	K562	blood:	n/a	n/a
8	CBX3	chr2:54483150-54483759	K562	blood:	n/a	n/a
9	CEBPB	chr2:54487241-54487487	HepG2	liver:	n/a	chr2:54487360-54487371
10	CEBPB	chr2:54489290-54489459	HepG2	liver:	n/a	chr2:54489390-54489401
11	CEBPB	chr2:54489231-54489564	HepG2	liver:	n/a	chr2:54489390-54489401
12	CEBPB	chr2:54489334-54489439	Hela-S3	cervix:	n/a	chr2:54489390-54489401
13	CEBPB	chr2:54482440-54482590	K562	blood:	n/a	n/a
14	CEBPB	chr2:54487244-54487489	A549	lung:	n/a	chr2:54487360-54487371
15	CEBPB	chr2:54489219-54489559	IMR90	lung:	n/a	chr2:54489390-54489401
16	CEBPB	chr2:54489322-54489472	A549	lung:	n/a	chr2:54489390-54489401
17	CHD1	chr2:54486422-54486518	GM12878	blood:	n/a	n/a
18	CHD2	chr2:54483070-54483827	K562	blood:	n/a	n/a
19	CHD2	chr2:54482759-54482864	K562	blood:	n/a	n/a
20	CREB1	chr2:54486444-54487023	GM12878	blood:	n/a	n/a
21	CREB1	chr2:54486521-54486984	GM12878	blood:	n/a	n/a
22	CTCF	chr2:54481480-54481630	HEK293	kidney:	n/a	n/a
23	CTCF	chr2:54481472-54481551	Gliobla	brain:	n/a	n/a
24	CTCF	chr2:54481440-54481590	BE2_C	brain:	n/a	n/a
25	CTCF	chr2:54481460-54481610	HFF-Myc	foreskin:	n/a	n/a
26	CTCF	chr2:54481400-54481550	WERI-Rb-1	eye:	n/a	n/a
27	CTCF	chr2:54481400-54481550	GM12868	blood:	n/a	n/a
28	CTCF	chr2:54481507-54481525	MCF-7	breast:	n/a	n/a
29	CTCF	chr2:54481360-54481510	HCT-116	colon:	n/a	n/a
30	CTCF	chr2:54481420-54481570	HA-sp	spinal cord:	n/a	n/a
31	CTCF	chr2:54481340-54481490	NB4	blood:	n/a	n/a
32	CTCF	chr2:54481464-54481584	A549	lung:	n/a	n/a
33	CTCF	chr2:54481400-54481550	RPTEC	kidney:	n/a	n/a
34	CTCF	chr2:54481400-54481550	GM12875	blood:	n/a	n/a
35	CTCF	chr2:54481440-54481590	K562	blood:	n/a	n/a
36	CTCF	chr2:54481393-54481700	K562	blood:	n/a	n/a
37	CTCF	chr2:54484256-54484334	GM10266	blood:	n/a	n/a
38	CTCF	chr2:54481420-54481570	GM12873	blood:	n/a	n/a
39	CTCF	chr2:54481524-54481563	GM19239	blood:	n/a	n/a
40	CTCF	chr2:54481461-54481589	HUVEC	blood vessel:	n/a	n/a
41	CTCF	chr2:54481498-54481577	IMR90	lung:	n/a	n/a
42	CTCF	chr2:54481344-54481748	K562	blood:	n/a	n/a
43	CTCF	chr2:54481329-54481701	HepG2	liver:	n/a	n/a
44	CTCF	chr2:54481520-54481670	A549	lung:	n/a	n/a
45	CTCF	chr2:54481392-54481679	HepG2	liver:	n/a	n/a
46	CTCF	chr2:54481268-54481831	K562	blood:	n/a	n/a
47	CTCF	chr2:54492375-54492396	Kidney_OC	kidney:	n/a	n/a
48	CTCF	chr2:54481400-54481550	HUVEC	blood vessel:	n/a	n/a
49	CTCF	chr2:54481440-54481590	HMF	breast:	n/a	n/a
50	CTCF	chr2:54481428-54481644	K562	blood:	n/a	n/a

(count:854 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:54481922-54481972	SK-N-SH	brain:	n/a
2	chr2:54482475-54482525	Caco-2	colon:	n/a
3	chr2:54483193-54483243	HL-60	blood:	n/a
4	chr2:54481922-54481972	PrEC	prostate:	n/a
5	chr2:54483341-54483391	HAEpiC	amniotic membrane:	n/a
6	chr2:54483498-54483548	NHBE	bronchial:	n/a
7	chr2:54485712-54485762	Caco-2	colon:	n/a
8	chr2:54483817-54483867	AG10803	skin:	n/a
9	chr2:54483379-54483429	U87	brain:	n/a
10	chr2:54483379-54483429	Jurkat	blood:	n/a
11	chr2:54483341-54483391	HRPEpiC	eye:	n/a
12	chr2:54481922-54481972	HCPEpiC	choroid plexus:	n/a
13	chr2:54482475-54482525	HMEC	breast:	n/a
14	chr2:54482841-54482891	HRPEpiC	eye:	n/a
15	chr2:54479214-54479264	HL-60	blood:	n/a
16	chr2:54483433-54483483	GM06990	blood:	n/a
17	chr2:54483619-54483669	IMR90	lung:	fetal
18	chr2:54483431-54483481	SKMC	muscle:	n/a
19	chr2:54482841-54482891	ECC-1	luminal epithelium:	n/a
20	chr2:54483498-54483548	GM12892	blood:	n/a
21	chr2:54479214-54479264	PFSK-1	brain:	n/a
22	chr2:54482841-54482891	PrEC	prostate:	n/a
23	chr2:54482475-54482525	CMK	blood:	n/a
24	chr2:54483431-54483481	PFSK-1	brain:	n/a
25	chr2:54483341-54483391	NB4	blood:	n/a
26	chr2:54483433-54483483	Jurkat	blood:	n/a
27	chr2:54482841-54482891	NB4	blood:	n/a
28	chr2:54483619-54483669	Hela-S3	cervix:	n/a
29	chr2:54483379-54483429	HUVEC	blood vessel:	n/a
30	chr2:54483379-54483429	ovcar-3	ovarian:	n/a
31	chr2:54483817-54483867	GM06990	blood:	n/a
32	chr2:54483817-54483867	AG04449	skin:	fetal
33	chr2:54483498-54483548	A549	lung:	n/a
34	chr2:54483379-54483429	HCPEpiC	choroid plexus:	n/a
35	chr2:54482841-54482891	HepG2	liver:	n/a
36	chr2:54483379-54483429	NT2-D1	testis:	n/a
37	chr2:54481922-54481972	GM12891	blood:	n/a
38	chr2:54483193-54483243	PFSK-1	brain:	n/a
39	chr2:54483619-54483669	AG04449	skin:	fetal
40	chr2:54483817-54483867	NT2-D1	testis:	n/a
41	chr2:54483193-54483243	AG09309	skin:	n/a
42	chr2:54483433-54483483	HRE	kidney:	n/a
43	chr2:54483431-54483481	HL-60	blood:	n/a
44	chr2:54483193-54483243	HIPEpiC	eye:	n/a
45	chr2:54483498-54483548	SK-N-SH_RA	brain:	n/a
46	chr2:54481922-54481972	K562	blood:	n/a
47	chr2:54483433-54483483	GM19239	blood:	n/a
48	chr2:54483193-54483243	SAEC	small airway:	n/a
49	chr2:54483619-54483669	SAEC	small airway:	n/a
50	chr2:54483193-54483243	HEEpiC	esophagus:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54483388..54485294-chr2:54487468..54489310,2	K562	blood:
2	chr2:54482506..54484137-chr2:54492737..54494268,2	K562	blood:
3	chr2:54340617..54344494-chr2:54480899..54484108,3	K562	blood:
4	chr2:54341887..54343531-chr2:54472985..54475968,2	K562	blood:
5	chr2:54466633..54468348-chr2:54481012..54483338,2	K562	blood:
6	chr2:54483794..54487067-chr2:54487468..54489708,3	K562	blood:
7	chr2:54483446..54484986-chr2:54498867..54501020,2	K562	blood:
8	chr2:53993157..53995066-chr2:54480511..54482787,2	K562	blood:
9	chr2:54483794..54487067-chr2:54487468..54489708,3	K562	blood:
10	chr2:54342108..54344179-chr2:54478859..54480893,2	K562	blood:
11	chr2:54470373..54472757-chr2:54474538..54476431,2	K562	blood:
12	chr2:54465360..54468834-chr2:54480824..54482850,3	K562	blood:

No data

Variant related genes	Relation type
TSPYL6	TF binding region
TSPYL6	CpG island
ENSG00000178021	chromatin interactions
ENSG00000143942	chromatin interactions
ENSG00000170634	chromatin interactions
ENSG00000115239	chromatin interactions

Extended variants
information (count: 911 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:911 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11125529	chr2:54475866-54475867	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance disease
2	rs563406735	chr2:54475873-54475874	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs12615749	chr2:54475885-54475886	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs565934649	chr2:54475894-54475895	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs12615793	chr2:54475914-54475915	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs548406645	chr2:54475934-54475935	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs73934415	chr2:54475962-54475963	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs6727644	chr2:54476019-54476020	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs192471220	chr2:54476101-54476102	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs376084826	chr2:54476116-54476117	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs376366310	chr2:54476159-54476160	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs558757059	chr2:54476213-54476214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs572162744	chr2:54476234-54476235	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs183870747	chr2:54476261-54476262	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs554814955	chr2:54476302-54476303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs554346823	chr2:54476314-54476315	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs574520427	chr2:54476345-54476346	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs550467305	chr2:54476350-54476351	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs187613760	chr2:54476426-54476427	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs74358552	chr2:54476435-54476436	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs577074714	chr2:54476439-54476440	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs546106908	chr2:54476452-54476453	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs559861198	chr2:54476465-54476466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs576356902	chr2:54476507-54476508	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs192103422	chr2:54476527-54476528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs182735943	chr2:54476528-54476529	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs531045974	chr2:54476545-54476546	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs55649227	chr2:54476572-54476573	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs398080269	chr2:54476586-54476587	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs397932745	chr2:54476587-54476588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs17045711	chr2:54476678-54476679	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs539531414	chr2:54476730-54476731	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs570881620	chr2:54476736-54476737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs187072146	chr2:54476741-54476742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs552485779	chr2:54476745-54476746	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs147757200	chr2:54476790-54476791	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs375295578	chr2:54476799-54476800	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs534514951	chr2:54476839-54476840	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs377370733	chr2:54476887-54476888	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs142516938	chr2:54476893-54476894	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs192343707	chr2:54477001-54477002	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs552405142	chr2:54477003-54477004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs7567531	chr2:54477027-54477028	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs375767536	chr2:54477103-54477104	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs371093458	chr2:54477104-54477105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs556509461	chr2:54477136-54477137	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs34195465	chr2:54477195-54477196	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs184275329	chr2:54477212-54477213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs189122957	chr2:54477217-54477218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs35990346	chr2:54477218-54477219	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:62)

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

Chromatin state (count:135 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:54452800-54490200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:54455800-54476000	Weak transcription	K562	blood
4	chr2:54456400-54487200	Weak transcription	Psoas Muscle	Psoas
5	chr2:54468400-54492200	Weak transcription	HSMMtube	muscle
6	chr2:54468600-54481600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:54469400-54480800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:54472800-54482400	Weak transcription	Fetal Stomach	stomach
9	chr2:54474200-54485600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:54474600-54478800	Weak transcription	HepG2	liver
11	chr2:54474600-54481800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:54474600-54482600	Weak transcription	Right Ventricle	heart
13	chr2:54474600-54484200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:54476000-54476200	ZNF genes & repeats	K562	blood
15	chr2:54476200-54478800	Weak transcription	K562	blood
16	chr2:54477800-54482800	Weak transcription	Pancreas	Pancrea
17	chr2:54478200-54478600	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr2:54478800-54479200	Enhancers	HepG2	liver
19	chr2:54478800-54479400	ZNF genes & repeats	K562	blood
20	chr2:54479200-54487200	Weak transcription	HepG2	liver
21	chr2:54479200-54489200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:54479400-54479600	Weak transcription	K562	blood
23	chr2:54479600-54480800	Active TSS	K562	blood
24	chr2:54479600-54482600	Weak transcription	Liver	Liver
25	chr2:54479800-54489200	Weak transcription	Gastric	stomach
26	chr2:54480000-54481600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr2:54480200-54482400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:54480400-54485400	Weak transcription	Fetal Lung	lung
29	chr2:54480600-54481000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:54480600-54481000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:54480600-54481600	Enhancers	Brain Substantia Nigra	brain
32	chr2:54480800-54481000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:54480800-54482000	Transcr. at gene 5' and 3'	K562	blood
34	chr2:54480800-54483400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:54481000-54482600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:54481000-54502600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:54481400-54481800	Weak transcription	Fetal Intestine Small	intestine
38	chr2:54481600-54482200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:54481600-54482800	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:54481600-54484200	Weak transcription	Brain Substantia Nigra	brain
41	chr2:54481600-54487200	Weak transcription	Spleen	Spleen
42	chr2:54481800-54483200	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:54481800-54483600	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr2:54482000-54483800	Active TSS	K562	blood
45	chr2:54482200-54482600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:54482200-54482800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:54482200-54482800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:54482400-54482600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr2:54482400-54483400	ZNF genes & repeats	Fetal Stomach	stomach
50	chr2:54482600-54483000	ZNF genes & repeats	Liver	Liver

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