Variant report

Variant	nsv546419
Chromosome Location	chr1:62650550-62656809
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:62650846-62651149	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:62650894-62651146	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:62650850-62651137	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:62650847-62651145	MCF10A-Er-Src	breast:	n/a	n/a
5	FOSL2	chr1:62650869-62651164	HepG2	liver:	n/a	n/a
6	JUND	chr1:62650660-62651331	SK-N-SH	brain:	n/a	chr1:62650988-62650999
7	JUND	chr1:62650918-62651143	HepG2	liver:	n/a	chr1:62650988-62650999
8	JUND	chr1:62650951-62651032	H1-hESC	embryonic stem cell:	n/a	chr1:62650988-62650999
9	MAX	chr1:62656643-62656653	HepG2	liver:	n/a	n/a

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

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

Extended variants
information (count: 285 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:285 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1316323	chr1:62650550-62650551	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs568870180	chr1:62650591-62650592	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs552317368	chr1:62650592-62650593	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs3066234	chr1:62650593-62650594	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs528174542	chr1:62650594-62650595	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs71752013	chr1:62650604-62650605	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs76718430	chr1:62650606-62650607	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs76871767	chr1:62650607-62650608	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs149519040	chr1:62650643-62650644	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs558465572	chr1:62650655-62650656	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs377609136	chr1:62650675-62650676	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs534239480	chr1:62650702-62650703	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs555886660	chr1:62650737-62650738	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs574154806	chr1:62650745-62650746	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs1112561	chr1:62650749-62650750	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs548046213	chr1:62650769-62650770	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs145847843	chr1:62650787-62650788	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs185953781	chr1:62650789-62650790	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs577599468	chr1:62650798-62650799	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs79543465	chr1:62650821-62650822	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs142757126	chr1:62650826-62650827	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs870906	chr1:62650853-62650854	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs147340265	chr1:62650881-62650882	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs191768698	chr1:62650893-62650894	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs10637263	chr1:62650920-62650921	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs35693102	chr1:62650921-62650922	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs397758796	chr1:62650930-62650931	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs147993842	chr1:62650931-62650932	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs577755055	chr1:62650951-62650952	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs142309931	chr1:62650952-62650953	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs550643843	chr1:62650992-62650993	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs569010255	chr1:62651014-62651015	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs12031405	chr1:62651018-62651019	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs183539662	chr1:62651044-62651045	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs141571615	chr1:62651060-62651061	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs111416336	chr1:62651069-62651070	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs566482094	chr1:62651183-62651184	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs150914497	chr1:62651213-62651214	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
39	rs555831668	chr1:62651214-62651215	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
40	rs372094804	chr1:62651227-62651228	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
41	rs139348026	chr1:62651256-62651257	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
42	rs533650197	chr1:62651303-62651304	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
43	rs538090465	chr1:62651304-62651305	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
44	rs556217853	chr1:62651347-62651348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs200600749	chr1:62651391-62651392	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs577688138	chr1:62651409-62651410	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs188241272	chr1:62651415-62651416	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs527251378	chr1:62651467-62651468	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs553712157	chr1:62651490-62651491	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs191333952	chr1:62651515-62651516	Weak transcription Enhancers	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:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62640600-62651200	Enhancers	H1 Cell Line	embryonic stem cell
2	chr1:62646600-62660400	Weak transcription	Right Atrium	heart
3	chr1:62649800-62651000	Weak transcription	Placenta	Placenta
4	chr1:62649800-62660000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:62650400-62651400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:62650400-62658400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:62650400-62658800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:62651000-62651200	Enhancers	Placenta	Placenta
9	chr1:62651400-62652000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:62652000-62660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:62656000-62657400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:62656800-62658600	Weak transcription	H1 Cell Line	embryonic stem cell

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