Variant report

Variant	esv1840893
Chromosome Location	chr4:1389304-1391235
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:1385707..1387814-chr4:1390928..1394108,3	K562	blood:
2	chr4:1391126..1393483-chr4:1395042..1398028,2	MCF-7	breast:
3	chr4:1391181..1394010-chr4:1399067..1401828,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKX1-1-1	chr4:1389420-1389500	NONHSAT094711

Variant related genes	Relation type
ENSG00000235608	chromatin interactions

Extended variants
information (count: 143 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:143 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13112754	chr4:1389304-1389305	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs13136287	chr4:1389309-1389310	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs534369529	chr4:1389311-1389312	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs1140011	chr4:1389323-1389324	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs572687139	chr4:1389334-1389335	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs13137870	chr4:1389340-1389341	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs13118336	chr4:1389344-1389345	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs142095345	chr4:1389353-1389354	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs146370789	chr4:1389354-1389355	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs571164794	chr4:1389361-1389362	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs78222806	chr4:1389366-1389367	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs35061485	chr4:1389371-1389372	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs35263928	chr4:1389375-1389376	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs148729919	chr4:1389384-1389385	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs374867542	chr4:1389385-1389386	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs576663931	chr4:1389393-1389394	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs34525526	chr4:1389397-1389398	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs543944569	chr4:1389398-1389399	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs142215664	chr4:1389399-1389400	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs147839649	chr4:1389404-1389405	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs113374471	chr4:1389408-1389409	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs541093494	chr4:1389410-1389411	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs141444125	chr4:1389418-1389419	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs557440144	chr4:1389425-1389426	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs199706071	chr4:1389429-1389430	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs145208075	chr4:1389433-1389434	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs201846658	chr4:1389435-1389436	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs35321918	chr4:1389439-1389440	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs569514802	chr4:1389443-1389444	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs530576391	chr4:1389448-1389449	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs149222149	chr4:1389481-1389482	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs138375760	chr4:1389482-1389483	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs202094706	chr4:1389484-1389485	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs372615048	chr4:1389500-1389501	ZNF genes & repeats Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs552712734	chr4:1389503-1389504	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs374903316	chr4:1389518-1389519	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs370222193	chr4:1389524-1389525	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs143447149	chr4:1389533-1389534	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs375041221	chr4:1389534-1389535	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs115895472	chr4:1389538-1389539	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs367966601	chr4:1389547-1389548	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs370690293	chr4:1389548-1389549	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs550303044	chr4:1389556-1389557	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs139000482	chr4:1389557-1389558	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs142260088	chr4:1389571-1389572	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs115679864	chr4:1389588-1389589	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs375014471	chr4:1389594-1389595	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs544074983	chr4:1389599-1389600	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs368420407	chr4:1389605-1389606	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs146895743	chr4:1389628-1389629	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:63)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	20932292	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Type 2 diabetes	21754918	CNVD

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1360800-1389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr4:1378400-1390400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:1380400-1390200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:1380400-1391000	Weak transcription	Right Ventricle	heart
5	chr4:1380400-1391200	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:1380400-1391400	Weak transcription	HepG2	liver
7	chr4:1380600-1390200	Weak transcription	Colonic Mucosa	Colon
8	chr4:1382200-1392200	Weak transcription	Psoas Muscle	Psoas
9	chr4:1382600-1389800	Weak transcription	HSMM	muscle
10	chr4:1382600-1390400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:1382800-1390000	Weak transcription	NHEK	skin
12	chr4:1382800-1390200	Weak transcription	Osteobl	bone
13	chr4:1382800-1391200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:1384400-1391200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr4:1384800-1389600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:1385200-1389600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr4:1385600-1390000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:1385800-1389800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:1386000-1391000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
20	chr4:1386200-1389400	ZNF genes & repeats	Esophagus	oesophagus
21	chr4:1386200-1389600	ZNF genes & repeats	Fetal Intestine Small	intestine
22	chr4:1386200-1389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:1386200-1390600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:1386400-1389600	Strong transcription	Brain Hippocampus Middle	brain
25	chr4:1386400-1389600	ZNF genes & repeats	Lung	lung
26	chr4:1386400-1391000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:1386400-1391200	ZNF genes & repeats	Fetal Stomach	stomach
28	chr4:1386600-1389400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:1386600-1389400	Strong transcription	Primary T cells from cord blood	blood
30	chr4:1386600-1389600	ZNF genes & repeats	Spleen	Spleen
31	chr4:1386800-1389400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:1386800-1389400	ZNF genes & repeats	Thymus	Thymus
33	chr4:1386800-1389800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:1387000-1389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:1387200-1390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:1387600-1389600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:1387600-1389600	ZNF genes & repeats	Pancreas	Pancrea
38	chr4:1387600-1389800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
39	chr4:1387600-1390000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:1387600-1390200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:1387600-1391200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:1387600-1391200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
43	chr4:1387600-1391200	ZNF genes & repeats	Dnd41	blood
44	chr4:1387800-1389400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:1387800-1389400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr4:1387800-1389800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:1387800-1390000	Strong transcription	A549	lung
48	chr4:1387800-1390600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:1387800-1391800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:1388000-1389600	Strong transcription	Placenta	Placenta

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