Variant report

Variant	nsv945341
Chromosome Location	chr1:227784745-227787384
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	CTCF	chr1:227786405-227786465	LNCaP	prostate:	n/a	n/a
2	GATA3	chr1:227787046-227787115	SH-SY5Y	brain:	n/a	n/a
3	KAP1	chr1:227784582-227784957	K562	blood:	n/a	n/a
4	SETDB1	chr1:227784819-227784949	U2OS	brain:	n/a	n/a
5	ZNF143	chr1:227784779-227784985	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD4-3	chr1:227786125-227786795	NONHSAT009929

Variant related genes	Relation type
ENSG00000225934	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:86 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547007998	chr1:227784769-227784770	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs568417291	chr1:227784823-227784824	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs535864485	chr1:227784874-227784875	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs556939591	chr1:227784924-227784925	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs566425099	chr1:227784947-227784948	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs36121687	chr1:227784971-227784972	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs575528157	chr1:227784999-227785000	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs539233156	chr1:227785003-227785004	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs374453368	chr1:227785008-227785009	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs527620598	chr1:227785023-227785024	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs189347218	chr1:227785035-227785036	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs568917028	chr1:227785044-227785045	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs59753688	chr1:227785064-227785065	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs373437750	chr1:227785083-227785084	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs377442224	chr1:227785105-227785106	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs561452706	chr1:227785160-227785161	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs551404747	chr1:227785173-227785174	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs571405239	chr1:227785174-227785175	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs192213068	chr1:227785187-227785188	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs2999741	chr1:227785205-227785206	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs553903442	chr1:227785225-227785226	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs78262834	chr1:227785249-227785250	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs537667007	chr1:227785484-227785485	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs6656746	chr1:227785527-227785528	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs531264822	chr1:227785569-227785570	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs112899175	chr1:227785587-227785588	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs9726691	chr1:227785624-227785625	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs2999742	chr1:227785677-227785678	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs184384368	chr1:227785678-227785679	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs115023496	chr1:227785703-227785704	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs6667937	chr1:227785716-227785717	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs550979021	chr1:227785718-227785719	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs569052444	chr1:227785739-227785740	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs116981521	chr1:227785759-227785760	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs557636928	chr1:227785823-227785824	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs141312706	chr1:227785849-227785850	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs2999743	chr1:227785906-227785907	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs555013418	chr1:227785945-227785946	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs189866127	chr1:227785946-227785947	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs2935146	chr1:227786033-227786034	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs376752089	chr1:227786039-227786040	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs181465855	chr1:227786044-227786045	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs575840610	chr1:227786082-227786083	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs201215838	chr1:227786202-227786203	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
45	rs201962841	chr1:227786203-227786204	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
46	rs546480590	chr1:227786213-227786214	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
47	rs564791274	chr1:227786255-227786256	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
48	rs186511698	chr1:227786256-227786257	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
49	rs12082414	chr1:227786257-227786258	Weak transcription ZNF genes & repeats	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs189312249	chr1:227786323-227786324	Weak transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Basal cell lymphoma	17053054	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Fumarase deficiency	21572526	CNVD
Autism	17483303	CNVD
Kartagener syndrome	16639409	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	22237106	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227771800-227790600	Weak transcription	Left Ventricle	heart
3	chr1:227774800-227790600	Weak transcription	Gastric	stomach
4	chr1:227774800-227799200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:227774800-227805000	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:227777200-227786000	Weak transcription	A549	lung
7	chr1:227777600-227790600	Weak transcription	Ovary	ovary
8	chr1:227779200-227799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:227781200-227800800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:227782400-227785600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:227782400-227788800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:227782800-227785200	ZNF genes & repeats	Dnd41	blood
13	chr1:227784000-227790600	Weak transcription	Aorta	Aorta
14	chr1:227784000-227798800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:227784000-227799600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:227784200-227787400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:227784200-227788200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:227784200-227788200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:227784200-227790600	Weak transcription	Pancreas	Pancrea
20	chr1:227784200-227793800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:227784200-227797800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:227784400-227794200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:227784800-227785200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:227785400-227787200	ZNF genes & repeats	Dnd41	blood
25	chr1:227786800-227787200	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr1:227787000-227788000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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