Variant report

Variant	esv3506795
Chromosome Location	chr4:1385371-1385575
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1233604..1236548-chr4:1385152..1387591,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKX1-1-2	chr4:1384734-1385606	NONHSAT094707

Variant related genes	Relation type
ENSG00000159692	chromatin interactions

Extended variants
information (count: 25 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs78436641	chr4:1385383-1385384	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs189871588	chr4:1385407-1385408	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs13135515	chr4:1385448-1385449	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs551000228	chr4:1385479-1385480	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs182088569	chr4:1385484-1385485	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs71168837	chr4:1385495-1385496	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs148500078	chr4:1385496-1385497	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs386670502	chr4:1385500-1385501	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs11726794	chr4:1385501-1385502	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	mRNA abundance
10	rs558978995	chr4:1385505-1385506	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs111271691	chr4:1385506-1385507	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs13141077	chr4:1385509-1385510	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs386670503	chr4:1385517-1385518	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs13107426	chr4:1385519-1385520	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs114064508	chr4:1385525-1385526	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs386670504	chr4:1385531-1385532	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs76713467	chr4:1385532-1385533	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs60789782	chr4:1385538-1385539	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs74454755	chr4:1385539-1385540	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs560406882	chr4:1385554-1385555	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs74869242	chr4:1385557-1385558	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs186286429	chr4:1385559-1385560	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs545584156	chr4:1385561-1385562	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs77415897	chr4:1385564-1385565	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs78170080	chr4:1385570-1385571	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1341800-1387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:1341800-1388800	Weak transcription	Small Intestine	intestine
3	chr4:1342600-1385600	Weak transcription	Fetal Kidney	kidney
4	chr4:1346000-1386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:1346000-1389200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:1360800-1389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:1368800-1389200	Weak transcription	NHDF-Ad	bronchial
8	chr4:1378400-1390400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:1378600-1389200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:1380200-1387200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:1380200-1387600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:1380200-1387800	Weak transcription	A549	lung
13	chr4:1380200-1388800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:1380400-1385400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:1380400-1386200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:1380400-1386400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:1380400-1387600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:1380400-1387600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:1380400-1387600	Weak transcription	Gastric	stomach
20	chr4:1380400-1387600	Weak transcription	NHLF	lung
21	chr4:1380400-1390200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:1380400-1391000	Weak transcription	Right Ventricle	heart
23	chr4:1380400-1391200	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:1380400-1391400	Weak transcription	HepG2	liver
25	chr4:1380600-1390200	Weak transcription	Colonic Mucosa	Colon
26	chr4:1380800-1385800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:1380800-1386200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:1380800-1386400	Weak transcription	Lung	lung
29	chr4:1380800-1387600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:1380800-1387600	Weak transcription	Pancreas	Pancrea
31	chr4:1381000-1387800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr4:1381200-1386600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:1381200-1387800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:1381400-1387600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:1381400-1387800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr4:1381400-1388800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:1381600-1385400	Weak transcription	Ovary	ovary
38	chr4:1381600-1385600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:1381600-1386200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:1381600-1386200	Weak transcription	Esophagus	oesophagus
41	chr4:1381600-1387600	Weak transcription	Brain Angular Gyrus	brain
42	chr4:1382200-1392200	Weak transcription	Psoas Muscle	Psoas
43	chr4:1382600-1389800	Weak transcription	HSMM	muscle
44	chr4:1382600-1390400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:1382800-1385400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:1382800-1386000	Weak transcription	Left Ventricle	heart
47	chr4:1382800-1386200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:1382800-1387800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr4:1382800-1388200	Weak transcription	Fetal Brain Male	brain
50	chr4:1382800-1388600	Weak transcription	HSMMtube	muscle

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