Variant report

Variant	esv3420490
Chromosome Location	chr1:62112664-62116962
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	ARID3A	chr1:62112891-62113154	HepG2	liver:	n/a	n/a
2	CEBPB	chr1:62113772-62113972	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr1:62113754-62113947	K562	blood:	n/a	n/a
4	FOXA1	chr1:62112873-62113092	HepG2	liver:	n/a	chr1:62113019-62113034
5	FOXA1	chr1:62112882-62113105	HepG2	liver:	n/a	chr1:62113019-62113034
6	FOXA1	chr1:62116307-62116558	T-47D	breast:	n/a	n/a
7	FOXA1	chr1:62112832-62113155	HepG2	liver:	n/a	chr1:62113019-62113034
8	FOXA1	chr1:62112903-62113098	HepG2	liver:	n/a	chr1:62113019-62113034
9	FOXA1	chr1:62116322-62116620	T-47D	breast:	n/a	n/a
10	FOXA2	chr1:62112881-62113100	HepG2	liver:	n/a	n/a
11	GATA3	chr1:62116359-62116578	T-47D	breast:	n/a	n/a
12	GATA3	chr1:62116259-62116598	T-47D	breast:	n/a	n/a
13	SPI1	chr1:62114351-62114789	HL-60	blood:	n/a	n/a
14	UBTF	chr1:62114417-62114490	K562	blood:	n/a	n/a
15	ZKSCAN1	chr1:62113790-62114420	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:62106350..62108369-chr1:62114638..62116326,2	K562	blood:
2	chr1:62110139..62113045-chr1:62113882..62116057,2	K562	blood:
3	chr1:62110139..62113045-chr1:62113882..62116057,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INADL-1	chr1:62113728-62113990	XLOC_000227

Variant related genes	Relation type
ENSG00000223920	TF binding region

Extended variants
information (count: 136 )
Associated
traits (count: 94 )

Variant overlapped rSNPs/rCNVs (count:136 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs373936941	chr1:62112677-62112678	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs369068355	chr1:62112682-62112683	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs544476602	chr1:62112699-62112700	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs7551993	chr1:62112740-62112741	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs74076280	chr1:62112744-62112745	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs376326661	chr1:62112747-62112748	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs12092067	chr1:62112763-62112764	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs536075835	chr1:62112883-62112884	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs527899981	chr1:62112903-62112904	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs192535812	chr1:62112928-62112929	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs561509483	chr1:62112978-62112979	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs531959515	chr1:62112987-62112988	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs550441251	chr1:62113063-62113064	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs565289740	chr1:62113080-62113081	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs532502925	chr1:62113093-62113094	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs547935833	chr1:62113095-62113096	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs566146530	chr1:62113097-62113098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs7544197	chr1:62113102-62113103	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs368109820	chr1:62113131-62113132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs398102776	chr1:62113132-62113133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs34083756	chr1:62113133-62113134	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs397693049	chr1:62113140-62113141	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs17378118	chr1:62113261-62113262	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs537756995	chr1:62113402-62113403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs550882468	chr1:62113425-62113426	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs10889247	chr1:62113442-62113443	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs577238051	chr1:62113443-62113444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs553234814	chr1:62113457-62113458	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs80245753	chr1:62113465-62113466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs150508798	chr1:62113484-62113485	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs139486146	chr1:62113498-62113499	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs368361420	chr1:62113532-62113533	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs533416704	chr1:62113550-62113551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs150051837	chr1:62113555-62113556	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs576540310	chr1:62113569-62113570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs12142692	chr1:62113597-62113598	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs569674820	chr1:62113628-62113629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs565552105	chr1:62113648-62113649	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs532568218	chr1:62113649-62113650	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs547848186	chr1:62113738-62113739	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs557281777	chr1:62113745-62113746	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs376623822	chr1:62113756-62113757	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs145410591	chr1:62113757-62113758	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs373565779	chr1:62113820-62113821	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs188838793	chr1:62113866-62113867	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs538013273	chr1:62113885-62113886	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs373276411	chr1:62113910-62113911	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs58126481	chr1:62113961-62113962	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs180810432	chr1:62113976-62113977	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs537050698	chr1:62113977-62113978	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:94)

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
Breast cancer	22522925	CNVD
Bipolar disorder	19114987	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62103400-62146400	Weak transcription	Gastric	stomach
2	chr1:62108000-62112800	Weak transcription	Ovary	ovary
3	chr1:62112400-62113000	Enhancers	Stomach Mucosa	stomach
4	chr1:62112600-62113000	Enhancers	HepG2	liver
5	chr1:62112800-62113000	Enhancers	Ovary	ovary
6	chr1:62114400-62115000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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