Variant report

Variant	nsv520333
Chromosome Location	chr1:62766527-62769887
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	E2F6	chr1:62767306-62768019	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:62767417-62767940	H1-hESC	embryonic stem cell:	n/a	chr1:62767575-62767586 chr1:62767574-62767587 chr1:62767575-62767585 chr1:62767576-62767585 chr1:62767576-62767586 chr1:62767576-62767586 chr1:62767574-62767589 chr1:62767567-62767583 chr1:62767576-62767586 chr1:62767575-62767586 chr1:62767577-62767586
3	MAX	chr1:62767412-62767698	K562	blood:	n/a	chr1:62767575-62767586 chr1:62767574-62767587 chr1:62767575-62767585 chr1:62767576-62767585 chr1:62767576-62767586 chr1:62767576-62767586 chr1:62767574-62767589 chr1:62767567-62767583 chr1:62767576-62767586 chr1:62767575-62767586 chr1:62767577-62767586
4	MAX	chr1:62767331-62768008	H1-hESC	embryonic stem cell:	n/a	chr1:62767575-62767586 chr1:62767574-62767587 chr1:62767575-62767585 chr1:62767576-62767585 chr1:62767576-62767586 chr1:62767576-62767586 chr1:62767574-62767589 chr1:62767567-62767583 chr1:62767576-62767586 chr1:62767575-62767586 chr1:62767577-62767586
5	MAX	chr1:62767387-62767805	H1-hESC	embryonic stem cell:	n/a	chr1:62767575-62767586 chr1:62767574-62767587 chr1:62767575-62767585 chr1:62767576-62767585 chr1:62767576-62767586 chr1:62767576-62767586 chr1:62767574-62767589 chr1:62767567-62767583 chr1:62767576-62767586 chr1:62767575-62767586 chr1:62767577-62767586
6	MAX	chr1:62767435-62767721	NB4	blood:	n/a	chr1:62767575-62767586 chr1:62767574-62767587 chr1:62767575-62767585 chr1:62767576-62767585 chr1:62767576-62767586 chr1:62767576-62767586 chr1:62767574-62767589 chr1:62767567-62767583 chr1:62767576-62767586 chr1:62767575-62767586 chr1:62767577-62767586
7	MYC	chr1:62767508-62767734	H1-hESC	embryonic stem cell:	n/a	chr1:62767575-62767586 chr1:62767574-62767587 chr1:62767575-62767585 chr1:62767576-62767585 chr1:62767576-62767586 chr1:62767576-62767586 chr1:62767574-62767589 chr1:62767567-62767583 chr1:62767576-62767586 chr1:62767575-62767586 chr1:62767577-62767586
8	POLR2A	chr1:62766532-62766947	H1-neurons	neurons:	n/a	n/a
9	USF1	chr1:62767428-62767766	H1-hESC	embryonic stem cell:	n/a	n/a
10	USF1	chr1:62767393-62767711	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RNU6-371P	TF binding region

Extended variants
information (count: 132 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:132 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1325742	chr1:62766527-62766528	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs572479272	chr1:62766535-62766536	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs542995550	chr1:62766547-62766548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs184872591	chr1:62766554-62766555	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs568818349	chr1:62766590-62766591	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs548455135	chr1:62766591-62766592	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs74076477	chr1:62766601-62766602	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs544469177	chr1:62766642-62766643	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs562778549	chr1:62766665-62766666	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs533124820	chr1:62766678-62766679	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs537355230	chr1:62766683-62766684	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs374367042	chr1:62766739-62766740	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs376740353	chr1:62766745-62766746	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs138063514	chr1:62766746-62766747	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs189500671	chr1:62766790-62766791	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs527428712	chr1:62766851-62766852	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs548961152	chr1:62766852-62766853	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs74076479	chr1:62766860-62766861	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs79256191	chr1:62766887-62766888	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs12718429	chr1:62766969-62766970	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs550248971	chr1:62766987-62766988	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs74076480	chr1:62767031-62767032	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs181448772	chr1:62767073-62767074	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs74811254	chr1:62767104-62767105	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs536389646	chr1:62767106-62767107	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs76772498	chr1:62767119-62767120	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs186184120	chr1:62767138-62767139	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs555047033	chr1:62767167-62767168	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs6675508	chr1:62767190-62767191	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs555150261	chr1:62767191-62767192	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs12089198	chr1:62767201-62767202	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs75330868	chr1:62767209-62767210	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs578019451	chr1:62767232-62767233	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs142433966	chr1:62767256-62767257	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs12058486	chr1:62767265-62767266	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs535550953	chr1:62767266-62767267	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs191288615	chr1:62767287-62767288	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs375192108	chr1:62767288-62767289	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs138390641	chr1:62767325-62767326	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs181224417	chr1:62767328-62767329	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs6675627	chr1:62767347-62767348	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs12079207	chr1:62767365-62767366	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs80030098	chr1:62767374-62767375	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs549395624	chr1:62767389-62767390	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs150528762	chr1:62767422-62767423	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs539006460	chr1:62767514-62767515	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs186696506	chr1:62767573-62767574	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs566091800	chr1:62767580-62767581	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs536336778	chr1:62767592-62767593	Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs138477593	chr1:62767622-62767623	Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:93)

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
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Chronic lymphocytic leukemia	21546498	CNVD

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
3	chr1:62761800-62767200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:62762000-62767000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:62762200-62767200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:62762200-62773200	Weak transcription	Fetal Lung	lung
7	chr1:62764800-62768000	Enhancers	Pancreas	Pancrea
8	chr1:62765000-62767000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:62765000-62767600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:62765000-62768000	Enhancers	Fetal Stomach	stomach
11	chr1:62765200-62766600	Enhancers	Brain Hippocampus Middle	brain
12	chr1:62765200-62767600	Genic enhancers	HepG2	liver
13	chr1:62765600-62766800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:62765600-62766800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr1:62765600-62767000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr1:62765600-62767800	Enhancers	Brain Substantia Nigra	brain
17	chr1:62765800-62766600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:62765800-62767000	Enhancers	Colon Smooth Muscle	Colon
19	chr1:62766000-62766800	Enhancers	Brain Angular Gyrus	brain
20	chr1:62766000-62767000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
21	chr1:62766000-62768600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:62766000-62770000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:62766000-62770200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:62766200-62766600	Weak transcription	Gastric	stomach
25	chr1:62766200-62767800	Weak transcription	Fetal Heart	heart
26	chr1:62766400-62766800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:62766400-62767600	Weak transcription	Fetal Kidney	kidney
28	chr1:62766600-62766800	Enhancers	Gastric	stomach
29	chr1:62766600-62767000	Enhancers	Stomach Smooth Muscle	stomach
30	chr1:62766600-62767200	Bivalent Enhancer	Brain Hippocampus Middle	brain
31	chr1:62766800-62767000	Bivalent Enhancer	Brain Angular Gyrus	brain
32	chr1:62766800-62767200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
33	chr1:62766800-62768000	Enhancers	H9 Cell Line	embryonic stem cell
34	chr1:62766800-62770200	Weak transcription	Gastric	stomach
35	chr1:62767000-62767600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
36	chr1:62767000-62768000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr1:62767000-62769000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:62767200-62767400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
39	chr1:62767200-62767600	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr1:62767200-62767600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:62767400-62767600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
42	chr1:62767400-62767600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
43	chr1:62767400-62768000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
44	chr1:62767600-62767800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
45	chr1:62767600-62767800	Bivalent Enhancer	Brain Angular Gyrus	brain
46	chr1:62767600-62768000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:62767600-62768000	Enhancers	Fetal Kidney	kidney
48	chr1:62767600-62780600	Weak transcription	HepG2	liver
49	chr1:62767800-62768000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
50	chr1:62767800-62768000	Enhancers	Fetal Heart	heart

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