Variant report

Variant	esv3395172
Chromosome Location	chr4:1388721-1389280
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKX1-1-1	chr4:1388324-1388811	NONHSAT094711
2	lnc-NKX1-1-1	chr4:1389149-1389169	NONHSAT094711

Extended variants
information (count: 155 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:155 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs76728908	chr4:1388724-1388725	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs199689156	chr4:1388726-1388727	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs9760383	chr4:1388728-1388729	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs146777511	chr4:1388738-1388739	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs539264269	chr4:1388743-1388744	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs555522174	chr4:1388745-1388746	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs78291991	chr4:1388750-1388751	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs373946226	chr4:1388755-1388756	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs150394202	chr4:1388756-1388757	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs138170890	chr4:1388757-1388758	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs112233131	chr4:1388759-1388760	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs375096873	chr4:1388768-1388769	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs369421055	chr4:1388769-1388770	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs372893833	chr4:1388772-1388773	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs573162478	chr4:1388774-1388775	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs146044439	chr4:1388780-1388781	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs138661466	chr4:1388781-1388782	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs141703556	chr4:1388785-1388786	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs146249377	chr4:1388786-1388787	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs577053657	chr4:1388788-1388789	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs142581445	chr4:1388789-1388790	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs79415192	chr4:1388790-1388791	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs76647382	chr4:1388793-1388794	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs562648546	chr4:1388795-1388796	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs139486277	chr4:1388800-1388801	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs548270390	chr4:1388805-1388806	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs537611982	chr4:1388808-1388809	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs150058646	chr4:1388811-1388812	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs559898855	chr4:1388812-1388813	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs200606324	chr4:1388817-1388818	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs142640592	chr4:1388818-1388819	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs144797159	chr4:1388819-1388820	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs374335051	chr4:1388821-1388822	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs147934929	chr4:1388830-1388831	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs9762123	chr4:1388831-1388832	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs148951627	chr4:1388836-1388837	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs569075815	chr4:1388839-1388840	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs74511366	chr4:1388848-1388849	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs78729943	chr4:1388850-1388851	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs377713366	chr4:1388851-1388852	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs148086093	chr4:1388852-1388853	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs76058011	chr4:1388867-1388868	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs115168119	chr4:1388874-1388875	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs75718523	chr4:1388879-1388880	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs74628005	chr4:1388881-1388882	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs201883654	chr4:1388882-1388883	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs138049268	chr4:1388883-1388884	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs562687352	chr4:1388886-1388887	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs79209471	chr4:1388891-1388892	Strong transcription ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs79550423	chr4:1388898-1388899	Strong transcription ZNF genes & repeats 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:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1341800-1388800	Weak transcription	Small Intestine	intestine
2	chr4:1346000-1389200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:1360800-1389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr4:1368800-1389200	Weak transcription	NHDF-Ad	bronchial
5	chr4:1378400-1390400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:1378600-1389200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:1380200-1388800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:1380400-1390200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:1380400-1391000	Weak transcription	Right Ventricle	heart
10	chr4:1380400-1391200	Weak transcription	Colon Smooth Muscle	Colon
11	chr4:1380400-1391400	Weak transcription	HepG2	liver
12	chr4:1380600-1390200	Weak transcription	Colonic Mucosa	Colon
13	chr4:1381400-1388800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:1382200-1392200	Weak transcription	Psoas Muscle	Psoas
15	chr4:1382600-1389800	Weak transcription	HSMM	muscle
16	chr4:1382600-1390400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:1382800-1390000	Weak transcription	NHEK	skin
18	chr4:1382800-1390200	Weak transcription	Osteobl	bone
19	chr4:1382800-1391200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:1384400-1391200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr4:1384800-1389600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:1385200-1389600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr4:1385600-1390000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:1385800-1389800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:1386000-1391000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr4:1386200-1388800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:1386200-1389000	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:1386200-1389200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:1386200-1389400	ZNF genes & repeats	Esophagus	oesophagus
30	chr4:1386200-1389600	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr4:1386200-1389800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:1386200-1390600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr4:1386400-1389000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
34	chr4:1386400-1389600	Strong transcription	Brain Hippocampus Middle	brain
35	chr4:1386400-1389600	ZNF genes & repeats	Lung	lung
36	chr4:1386400-1391000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr4:1386400-1391200	ZNF genes & repeats	Fetal Stomach	stomach
38	chr4:1386600-1388800	ZNF genes & repeats	Fetal Intestine Large	intestine
39	chr4:1386600-1389400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:1386600-1389400	Strong transcription	Primary T cells from cord blood	blood
41	chr4:1386600-1389600	ZNF genes & repeats	Spleen	Spleen
42	chr4:1386800-1389200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:1386800-1389400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr4:1386800-1389400	ZNF genes & repeats	Thymus	Thymus
45	chr4:1386800-1389800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:1387000-1389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:1387200-1390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:1387600-1389600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr4:1387600-1389600	ZNF genes & repeats	Pancreas	Pancrea
50	chr4:1387600-1389800	ZNF genes & repeats	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links