Variant report

Variant	esv3389807
Chromosome Location	chr5:1949052-1953850
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1799132..1801458-chr5:1950722..1953001,2	K562	blood:
2	chr5:1799852..1801806-chr5:1950738..1953312,2	MCF-7	breast:
3	chr5:1851660..1854180-chr5:1947393..1949890,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDUFS6-5	chr5:1948808-1949182	XLOC_004250

Variant related genes	Relation type
ENSG00000171421	chromatin interactions
ENSG00000145494	chromatin interactions

Extended variants
information (count: 261 )
Associated
traits (count: 112 )

Variant overlapped rSNPs/rCNVs (count:261 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs142165212	chr5:1949057-1949058	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
2	rs972972	chr5:1949082-1949083	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
3	rs559605789	chr5:1949093-1949094	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
4	rs74628165	chr5:1949098-1949099	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
5	rs542222317	chr5:1949107-1949108	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
6	rs548317385	chr5:1949113-1949114	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
7	rs113510261	chr5:1949134-1949135	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
8	rs398108512	chr5:1949136-1949137	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
9	rs369915180	chr5:1949188-1949189	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs149748856	chr5:1949193-1949194	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs6148877	chr5:1949194-1949195	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs201289957	chr5:1949195-1949196	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs28712296	chr5:1949210-1949211	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs529086890	chr5:1949237-1949238	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs531677454	chr5:1949265-1949266	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs560270953	chr5:1949332-1949333	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs972973	chr5:1949340-1949341	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs571518789	chr5:1949406-1949407	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs541568464	chr5:1949438-1949439	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs139398138	chr5:1949445-1949446	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs13187986	chr5:1949468-1949469	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs565666374	chr5:1949476-1949477	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs536330564	chr5:1949489-1949490	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs376889311	chr5:1949490-1949491	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs554187946	chr5:1949494-1949495	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs575631764	chr5:1949495-1949496	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
27	rs149533822	chr5:1949511-1949512	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
28	rs368638685	chr5:1949514-1949515	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
29	rs10064753	chr5:1949516-1949517	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs7736516	chr5:1949531-1949532	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs375950636	chr5:1949547-1949548	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs7736642	chr5:1949562-1949563	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs13174844	chr5:1949580-1949581	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs144165381	chr5:1949590-1949591	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs146524220	chr5:1949624-1949625	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs542300115	chr5:1949645-1949646	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs528014811	chr5:1949705-1949706	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs563719256	chr5:1949712-1949713	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs368764945	chr5:1949715-1949716	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs10074172	chr5:1949753-1949754	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs34486860	chr5:1949801-1949802	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs34170076	chr5:1949809-1949810	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs116034890	chr5:1949833-1949834	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs547311595	chr5:1949842-1949843	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs77461404	chr5:1949857-1949858	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs191366129	chr5:1949860-1949861	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs547887286	chr5:1949947-1949948	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs556881487	chr5:1949950-1949951	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs536662646	chr5:1949993-1949994	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs558099487	chr5:1950007-1950008	Weak transcription Enhancers Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:112)

Disease	PMID	Source
Biliary cancer	19435499	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16608533	CNVD
Cervical cancer	16585170	CNVD
Glioblastoma multiforme	22286061	CNVD
Lung cancer	17925434	CNVD
Ovarian cancer	20844748	CNVD
Cervical squamous cell carcinoma	21590768	CNVD
Non-small cell lung cancer	21829676	CNVD
Intracranial ependymoma	16609018	CNVD
Breast cancer	19181860	CNVD
prenatal diagnosis	20453657	CNVD
Developmental delay	19490664	CNVD
Human papillomavirus	17975027	CNVD
Acute monocytic leukemia	16498392	CNVD
Gastric cancer	16891809	CNVD
Intracranial aneurysm	16715129	CNVD
Emphysema	19352772	CNVD
Chordoma	18071362	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Lung cancer	21911935	CNVD
Cri-du chat syndrome	21549014	CNVD
Melanoma	18172304	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Sudden cardiac death	19188705	CNVD
renal disease	17924346	CNVD
abnormal development	18461090	CNVD
Lung cancer	19547694	CNVD
Cri-du chat syndrome	22283845	CNVD
Disorders of sex development	21048976	CNVD
Non-small cell lung cancer	20864512	CNVD
Cancer	21183584	CNVD
Honadal dysgenesis	21048976	CNVD
Cancer	16751803	CNVD
Breast cancer	17133270	CNVD
Hepatocellular carcinoma	22174799	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Salivary gland tumor	18059337	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Kartagener syndrome	16639409	CNVD
Medulloblastoma	21979893	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	16783165	CNVD
Thyroid cancer	19087340	CNVD
Liposarcoma	21253554	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cervical Cancer	21857958	CNVD
Cervical cancer	21062161	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Oral cancer	21386901	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Ewing''s sarcoma	17952124	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Cervical cancer	18559093	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	21364760	CNVD
Cancer	20164919	CNVD
Oral cancer	22144094	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Urothelial carcinoma	21177765	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Multiple myeloma	17550852	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Developmental delay	21147756	CNVD
prenatal diagnosis	22389664	CNVD
Bladder cancer	21909424	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Breast cancer	21858162	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Melanoma	22183965	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	22495311	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Schizophrenia	23813976	CNVD
Ependymoma	20639864	CNVD

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1932000-1950800	Weak transcription	Gastric	stomach
2	chr5:1935600-1950800	Weak transcription	Pancreas	Pancrea
3	chr5:1939000-1965600	Weak transcription	Brain Angular Gyrus	brain
4	chr5:1942600-1953800	Weak transcription	Ovary	ovary
5	chr5:1946800-1951800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:1947000-1951600	Enhancers	Fetal Heart	heart
7	chr5:1947200-1952200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:1948400-1949200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:1948400-1950000	Enhancers	Right Ventricle	heart
10	chr5:1948400-1950600	Bivalent Enhancer	Fetal Stomach	stomach
11	chr5:1948600-1949400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr5:1948600-1949600	Enhancers	Right Atrium	heart
13	chr5:1948600-1950200	Active TSS	Stomach Smooth Muscle	stomach
14	chr5:1948800-1949200	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr5:1948800-1949400	Active TSS	Colon Smooth Muscle	Colon
16	chr5:1949000-1949200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:1949000-1949200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:1949000-1949200	Flanking Active TSS	Fetal Muscle Leg	muscle
19	chr5:1949000-1949200	Active TSS	Left Ventricle	heart
20	chr5:1949000-1949200	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr5:1949000-1949200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
22	chr5:1949000-1949400	Bivalent Enhancer	A549	lung
23	chr5:1949000-1949600	Flanking Active TSS	Esophagus	oesophagus
24	chr5:1949000-1949600	Flanking Active TSS	NHEK	skin
25	chr5:1949000-1949800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:1949000-1949800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:1949000-1949800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:1949000-1949800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr5:1949000-1949800	Flanking Active TSS	HMEC	breast
30	chr5:1949000-1950600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr5:1949200-1949400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr5:1949200-1949400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:1949200-1949400	Enhancers	Fetal Muscle Leg	muscle
34	chr5:1949200-1949600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:1949200-1949600	Flanking Active TSS	Left Ventricle	heart
36	chr5:1949200-1949800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr5:1949200-1950800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:1949400-1950200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr5:1949400-1950600	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr5:1949400-1951400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr5:1949600-1949800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:1949600-1949800	Active TSS	Esophagus	oesophagus
43	chr5:1949600-1950200	Enhancers	NHEK	skin
44	chr5:1949600-1950600	Weak transcription	Left Ventricle	heart
45	chr5:1949800-1950000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:1949800-1950200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr5:1949800-1950200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:1949800-1950600	Weak transcription	Esophagus	oesophagus
49	chr5:1949800-1950600	Enhancers	HMEC	breast
50	chr5:1949800-1960600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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