Variant report

Variant	esv3338263
Chromosome Location	chr20:23981552-23985850
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	chr20:23979873..23982563-chr20:23986456..23988446,2	MCF-7	breast:
2	chr20:23976507..23978682-chr20:23981230..23983499,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GGTLC1-6	chr20:23982712-23982840	NONHSAT079094
2	lnc-GGTLC1-6	chr20:23983714-23983891	NONHSAT079094

Extended variants
information (count: 159 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:159 , 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	rs6076173	chr20:23982739-23982740	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs113895524	chr20:23982742-23982743	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs565453416	chr20:23982769-23982770	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs559688108	chr20:23982833-23982834	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs6049299	chr20:23983042-23983043	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs538035889	chr20:23983054-23983055	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs554514833	chr20:23983076-23983077	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs568325533	chr20:23983106-23983107	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs534118350	chr20:23983145-23983146	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs139807693	chr20:23983170-23983171	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs573298142	chr20:23983217-23983218	Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs545470325	chr20:23983218-23983219	Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs559018454	chr20:23983227-23983228	Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs34760340	chr20:23983229-23983230	Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs145294710	chr20:23983290-23983291	Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs76011084	chr20:23983400-23983401	Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs561350011	chr20:23983414-23983415	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs187181589	chr20:23983434-23983435	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs538636341	chr20:23983498-23983499	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs6114403	chr20:23983534-23983535	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs191255383	chr20:23983581-23983582	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs559690856	chr20:23983593-23983594	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs531991190	chr20:23983598-23983599	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs551796868	chr20:23983599-23983600	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs568931332	chr20:23983611-23983612	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
26	rs553786028	chr20:23983616-23983617	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
27	rs117653854	chr20:23983622-23983623	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
28	rs375424231	chr20:23983623-23983624	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
29	rs564024747	chr20:23983635-23983636	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
30	rs182944197	chr20:23983659-23983660	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
31	rs568181259	chr20:23983665-23983666	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
32	rs554696923	chr20:23983667-23983668	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
33	rs531144435	chr20:23983668-23983669	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
34	rs188042194	chr20:23983678-23983679	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
35	rs554113586	chr20:23983682-23983683	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
36	rs576570630	chr20:23983684-23983685	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
37	rs566830133	chr20:23983685-23983686	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
38	rs539023375	chr20:23983686-23983687	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
39	rs544035683	chr20:23983687-23983688	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
40	rs575669156	chr20:23983691-23983692	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
41	rs555984159	chr20:23983697-23983698	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
42	rs537987572	chr20:23983698-23983699	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
43	rs555109506	chr20:23983700-23983701	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
44	rs574713427	chr20:23983702-23983703	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
45	rs540485274	chr20:23983705-23983706	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
46	rs367656526	chr20:23983706-23983707	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
47	rs371267274	chr20:23983719-23983720	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	lncRNA	n/a	Overlapped CNVs	n/a
48	rs8124201	chr20:23983723-23983724	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs544662038	chr20:23983724-23983725	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	lncRNA	n/a	Overlapped CNVs	n/a
50	rs577165232	chr20:23983736-23983737	Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
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
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Breast cancer	16608533	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	17133270	CNVD
Thrombophilia	17576883	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Hepatocellular carcinoma	22174799	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23983000-23983200	Enhancers	Esophagus	oesophagus
2	chr20:23983000-23983800	Enhancers	Dnd41	blood
3	chr20:23983200-23983400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
4	chr20:23983600-23983800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr20:23983600-23983800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:23983600-23983800	ZNF genes & repeats	Fetal Kidney	kidney
7	chr20:23983600-23983800	Enhancers	Pancreas	Pancrea
8	chr20:23983600-23984000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr20:23983600-23984000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr20:23983600-23984000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:23983600-23984000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:23983600-23984000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr20:23983800-23984000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr20:23983800-23985800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:23983800-23986000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr20:23983800-23991600	Weak transcription	Fetal Kidney	kidney
17	chr20:23984000-23984600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr20:23984000-23985200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr20:23984000-23985200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:23984000-23985200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:23984000-23989200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr20:23984200-23986000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr20:23984400-23985600	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr20:23984600-23985000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:23985000-23985600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr20:23985000-23985600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr20:23985000-23985600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr20:23985000-23985800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr20:23985200-23985400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr20:23985200-23985600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr20:23985200-23985800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr20:23985800-23987400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr20:23985800-23992000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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