Variant report

Variant	nsv525956
Chromosome Location	chr20:16593159-16601519
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:16593627..16595980-chr20:16599044..16601255,2	MCF-7	breast:
2	chr20:16593627..16595980-chr20:16599044..16601255,2	MCF-7	breast:
3	chr20:16552663..16555302-chr20:16594757..16597060,2	MCF-7	breast:
4	chr20:16589932..16591784-chr20:16595469..16597980,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNRPB2-1	chr20:16593321-16594313	XLOC_013467
2	lnc-SNRPB2-1	chr20:16593029-16594313	XLOC_013467

No data

Variant related genes	Relation type
ENSG00000089177	chromatin interactions

Extended variants
information (count: 336 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:336 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1105853	chr20:16593159-16593160	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs190799359	chr20:16593189-16593190	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs184225691	chr20:16593209-16593210	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs561148398	chr20:16593210-16593211	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs13045815	chr20:16593261-16593262	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs370050128	chr20:16593294-16593295	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs559299005	chr20:16593344-16593345	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs572891341	chr20:16593485-16593486	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs200194759	chr20:16593487-16593488	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs540197419	chr20:16593501-16593502	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs564832090	chr20:16593528-16593529	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs147275963	chr20:16593554-16593555	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs76104887	chr20:16593557-16593558	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs563126681	chr20:16593561-16593562	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs530216997	chr20:16593578-16593579	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs140785477	chr20:16593596-16593597	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs538744688	chr20:16593597-16593598	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs374847345	chr20:16593630-16593631	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs533937867	chr20:16593660-16593661	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs552505875	chr20:16593696-16593697	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs570750233	chr20:16593697-16593698	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs538380869	chr20:16593741-16593742	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs555528450	chr20:16593779-16593780	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs372498853	chr20:16593793-16593794	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs16997969	chr20:16593803-16593804	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs558355173	chr20:16593813-16593814	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs575540987	chr20:16593821-16593822	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs144441459	chr20:16593830-16593831	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs554924458	chr20:16593903-16593904	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs573128204	chr20:16593915-16593916	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs147819632	chr20:16593934-16593935	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs564935297	chr20:16593969-16593970	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs187558676	chr20:16593995-16593996	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs114280482	chr20:16594034-16594035	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs141480550	chr20:16594107-16594108	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs530252844	chr20:16594118-16594119	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs548331356	chr20:16594122-16594123	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs560425142	chr20:16594126-16594127	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs528030966	chr20:16594156-16594157	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs112061949	chr20:16594215-16594216	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs559887699	chr20:16594244-16594245	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs570850827	chr20:16594270-16594271	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs78124619	chr20:16594274-16594275	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs145043133	chr20:16594275-16594276	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs544691990	chr20:16594287-16594288	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs149035607	chr20:16594300-16594301	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs536453833	chr20:16594312-16594313	Weak transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs554763824	chr20:16594314-16594315	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs573064119	chr20:16594329-16594330	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs534122920	chr20:16594371-16594372	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Glaucoma	21310917	CNVD
Alagille syndrome	22470819	CNVD
Lung cancer	16773561	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Myelofibrosis	22110671	CNVD
Kabuki syndrome	21720541	CNVD
Glioblastoma multiforme	22286061	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Neurocytoma	17123091	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	21364760	CNVD
lymphocytic leukemia	21291569	CNVD

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16587000-16593200	Enhancers	Fetal Intestine Large	intestine
2	chr20:16589200-16596000	Weak transcription	Colon Smooth Muscle	Colon
3	chr20:16589400-16593400	Weak transcription	HSMMtube	muscle
4	chr20:16589800-16596200	Weak transcription	Fetal Kidney	kidney
5	chr20:16590000-16596000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr20:16590000-16596400	Weak transcription	Ovary	ovary
7	chr20:16590000-16602400	Weak transcription	Right Atrium	heart
8	chr20:16590400-16595800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:16590400-16595800	Weak transcription	Small Intestine	intestine
10	chr20:16590400-16596200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr20:16590600-16594000	Weak transcription	Fetal Brain Male	brain
12	chr20:16590800-16595400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr20:16592200-16597000	Enhancers	Fetal Muscle Leg	muscle
14	chr20:16592400-16594400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr20:16592600-16597400	Enhancers	Fetal Lung	lung
16	chr20:16592600-16597600	Enhancers	Fetal Stomach	stomach
17	chr20:16592800-16593200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr20:16593000-16595800	Weak transcription	Fetal Intestine Small	intestine
19	chr20:16593000-16596000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr20:16593000-16596400	Weak transcription	Colonic Mucosa	Colon
21	chr20:16593200-16593800	Enhancers	Fetal Muscle Trunk	muscle
22	chr20:16593200-16595800	Weak transcription	Fetal Intestine Large	intestine
23	chr20:16593400-16594200	Enhancers	HSMMtube	muscle
24	chr20:16593600-16594000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr20:16593600-16594200	Enhancers	HSMM	muscle
26	chr20:16593600-16594400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr20:16593800-16594400	Enhancers	Stomach Smooth Muscle	stomach
28	chr20:16594000-16594400	Enhancers	Fetal Brain Male	brain
29	chr20:16594200-16595800	Weak transcription	HSMM	muscle
30	chr20:16594200-16596000	Weak transcription	HSMMtube	muscle
31	chr20:16594400-16594800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr20:16594400-16595400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr20:16594400-16596200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr20:16594400-16596400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr20:16595400-16595600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr20:16595400-16596400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:16595400-16596600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr20:16595400-16596800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr20:16595600-16596400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr20:16595600-16596600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr20:16595800-16596000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr20:16595800-16596200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr20:16595800-16596600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr20:16595800-16596600	Enhancers	Fetal Intestine Large	intestine
45	chr20:16595800-16596600	Enhancers	Rectal Smooth Muscle	rectum
46	chr20:16595800-16596600	Enhancers	HSMM	muscle
47	chr20:16595800-16596800	Enhancers	Hela-S3	cervix
48	chr20:16595800-16597000	Enhancers	Fetal Intestine Small	intestine
49	chr20:16595800-16597000	Enhancers	Small Intestine	intestine
50	chr20:16596000-16596400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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