Variant report

Variant	nsv819557
Chromosome Location	chr1:62652920-62657976
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:62)
Chromatin interactive
region (count:0)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:62657260-62657410	HepG2	liver:	n/a	n/a
2	MAX	chr1:62656643-62656653	HepG2	liver:	n/a	n/a
3	PAX5	chr1:62657643-62657810	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:62657841-62657963	H1-hESC	embryonic stem cell:	n/a	n/a
5	STAT3	chr1:62657352-62657552	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:62657689-62657739	Caco-2	colon:	n/a
2	chr1:62657689-62657739	Caco-2	colon:	n/a
3	chr1:62657689-62657739	AoSMC	blood vessel:	n/a
4	chr1:62657689-62657739	MCF-7	breast:	n/a
5	chr1:62657689-62657739	AG09319	gingival:	n/a
6	chr1:62657689-62657739	HCT-116	colon:	n/a
7	chr1:62657689-62657739	SK-N-MC	brain:	n/a
8	chr1:62657689-62657739	IMR90	lung:	fetal
9	chr1:62657689-62657739	Jurkat	blood:	n/a
10	chr1:62657689-62657739	ProgFib	skin:	n/a
11	chr1:62657689-62657739	H1-hESC	embryonic stem cell:	embryo
12	chr1:62657689-62657739	U87	brain:	n/a
13	chr1:62657689-62657739	HCF	heart:	n/a
14	chr1:62657689-62657739	HCPEpiC	choroid plexus:	n/a
15	chr1:62657689-62657739	NHBE	bronchial:	n/a
16	chr1:62657689-62657739	HRE	kidney:	n/a
17	chr1:62657689-62657739	PrEC	prostate:	n/a
18	chr1:62657689-62657739	NB4	blood:	n/a
19	chr1:62657689-62657739	GM12878	blood:	n/a
20	chr1:62657689-62657739	PANC-1	pancreas:	n/a
21	chr1:62657689-62657739	T-47D	breast:	n/a
22	chr1:62657689-62657739	NH-A	brain:	n/a
23	chr1:62657689-62657739	HNPCEpiC	eye:	n/a
24	chr1:62657689-62657739	Hepatocyte	liver:	n/a
25	chr1:62657689-62657739	HEK293	kidney:	embryo
26	chr1:62657689-62657739	ECC-1	luminal epithelium:	n/a
27	chr1:62657689-62657739	AG09309	skin:	n/a
28	chr1:62657689-62657739	Hela-S3	cervix:	n/a
29	chr1:62657689-62657739	AG04449	skin:	fetal
30	chr1:62657689-62657739	LNCaP	prostate:	n/a
31	chr1:62657689-62657739	A549	lung:	n/a
32	chr1:62657689-62657739	GM06990	blood:	n/a
33	chr1:62657689-62657739	SK-N-SH	brain:	n/a
34	chr1:62657689-62657739	HMEC	breast:	n/a
35	chr1:62657689-62657739	GM19239	blood:	n/a
36	chr1:62657689-62657739	RPTEC	kidney:	n/a
37	chr1:62657689-62657739	PFSK-1	brain:	n/a
38	chr1:62657689-62657739	HAEpiC	amniotic membrane:	n/a
39	chr1:62657689-62657739	AG10803	skin:	n/a
40	chr1:62657689-62657739	SK-N-SH_RA	brain:	n/a
41	chr1:62657689-62657739	BE2_C	brain:	n/a
42	chr1:62657689-62657739	HRCEpiC	kidney:	n/a
43	chr1:62657689-62657739	HIPEpiC	eye:	n/a
44	chr1:62657689-62657739	ovcar-3	ovarian:	n/a
45	chr1:62657689-62657739	MCF10A-Er-Src	breast:	n/a
46	chr1:62657689-62657739	AG04450	lung:	fetal
47	chr1:62657689-62657739	SKMC	muscle:	n/a
48	chr1:62657689-62657739	K562	blood:	n/a
49	chr1:62657689-62657739	GM12891	blood:	n/a
50	chr1:62657689-62657739	HPAEpiC	pulmonary alveolar:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-L1TD1-1	chr1:62656194-62656598	NONHSAT003628
2	lnc-L1TD1-2	chr1:62654803-62655175	NONHSAT003627
3	lnc-L1TD1-2	chr1:62655541-62655625	NONHSAT003627

No data

Variant related genes	Relation type
RPS15AP7	TF binding region
L1TD1	TF binding region
PIGPP2	TF binding region
RPS15AP7	CpG island
L1TD1	CpG island
PIGPP2	CpG island

Extended variants
information (count: 239 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:239 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536763968	chr1:62652935-62652936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs554624804	chr1:62652951-62652952	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs183340200	chr1:62652956-62652957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs576385911	chr1:62653029-62653030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs555777897	chr1:62653034-62653035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs139709901	chr1:62653038-62653039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs112983540	chr1:62653054-62653055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs200050864	chr1:62653063-62653064	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs557122355	chr1:62653064-62653065	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs371699792	chr1:62653065-62653066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs577894700	chr1:62653066-62653067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs28878237	chr1:62653077-62653078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs376667333	chr1:62653078-62653079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs4915798	chr1:62653083-62653084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs11207920	chr1:62653086-62653087	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs74764142	chr1:62653087-62653088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs575733496	chr1:62653104-62653105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs572011417	chr1:62653105-62653106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs542717593	chr1:62653128-62653129	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs560676632	chr1:62653132-62653133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs376922798	chr1:62653139-62653140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs188917605	chr1:62653164-62653165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs142296589	chr1:62653198-62653199	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs565274206	chr1:62653212-62653213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs193067357	chr1:62653225-62653226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs185357055	chr1:62653237-62653238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs563656981	chr1:62653250-62653251	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs528037813	chr1:62653252-62653253	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs145916090	chr1:62653292-62653293	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs536300504	chr1:62653317-62653318	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs548682715	chr1:62653319-62653320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs2457818	chr1:62653341-62653342	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs34626505	chr1:62653369-62653370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs558645118	chr1:62653388-62653389	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs576951408	chr1:62653401-62653402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs138832098	chr1:62653451-62653452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs141227643	chr1:62653456-62653457	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs189809929	chr1:62653485-62653486	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs538949785	chr1:62653510-62653511	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs191791385	chr1:62653511-62653512	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs113945343	chr1:62653542-62653543	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs183682235	chr1:62653543-62653544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs542356001	chr1:62653562-62653563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs11207921	chr1:62653571-62653572	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs576931058	chr1:62653610-62653611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs188343386	chr1:62653645-62653646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs528397061	chr1:62653647-62653648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs543044403	chr1:62653652-62653653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs564563560	chr1:62653692-62653693	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs77428809	chr1:62653714-62653715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Breast cancer	16620391	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
CNS Malformation Syndrome	17530927	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Colorectal cancer	20459617	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62646600-62660400	Weak transcription	Right Atrium	heart
2	chr1:62649800-62660000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:62650400-62658400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:62650400-62658800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:62652000-62660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:62656000-62657400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:62656800-62658600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:62657000-62657200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:62657200-62657400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:62657200-62657400	Bivalent Enhancer	K562	blood
11	chr1:62657400-62657600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:62657400-62657600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr1:62657400-62657600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:62657400-62658400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:62657400-62659000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:62657600-62658400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:62657600-62660000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:62657600-62660000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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