Variant report

Variant	esv3431790
Chromosome Location	chr20:12940407-12948115
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:7)
LncRNA
region (count:12)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:12941463..12943706-chr20:12945619..12947454,2	MCF-7	breast:
2	chr2:201161815..201162676-chr20:12942962..12943611,2	MCF-7	breast:
3	chr20:12906070..12908369-chr20:12946069..12948002,2	MCF-7	breast:
4	chr20:12904584..12906657-chr20:12946403..12948442,2	MCF-7	breast:
5	chr20:12905418..12906763-chr20:12946186..12947828,17	MCF-7	breast:
6	chr20:12905518..12906454-chr20:12946845..12948133,8	MCF-7	breast:
7	chr20:12941463..12943706-chr20:12945619..12947454,2	MCF-7	breast:

(count:12 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPTLC3-1	chr20:12947694-12947858	XLOC_013465
2	lnc-SPTLC3-1	chr20:12947694-12947858	XLOC_013465
3	lnc-SPTLC3-1	chr20:12946646-12946820	NONHSAT078674
4	lnc-SPTLC3-1	chr20:12947694-12947847	NONHSAT078674
5	lnc-SPTLC3-1	chr20:12947697-12947858	NONHSAT078665
6	lnc-SPTLC3-1	chr20:12946729-12946820	XLOC_013465
7	lnc-SPTLC3-1	chr20:12946650-12946820	NONHSAT078664
8	lnc-SPTLC3-1	chr20:12946646-12946820	XLOC_013465
9	lnc-SPTLC3-1	chr20:12946729-12946820	XLOC_013465
10	lnc-SPTLC3-1	chr20:12947694-12947858	NONHSAT078664
11	lnc-SPTLC3-1	chr20:12946581-12946820	NONHSAT078665
12	lnc-SPTLC3-1	chr20:12947694-12947891	XLOC_013465

No data

Variant related genes	Relation type
ITGB2	miRNA target sites
NNT	miRNA target sites

Extended variants
information (count: 272 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:272 , 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	rs531422639	chr20:12940424-12940425	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs182966670	chr20:12940432-12940433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs557252251	chr20:12940482-12940483	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs114823715	chr20:12940490-12940491	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs573752878	chr20:12940515-12940516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs113389539	chr20:12940527-12940528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs553776107	chr20:12940578-12940579	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs559678763	chr20:12940601-12940602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs6105003	chr20:12940613-12940614	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs386812625	chr20:12940649-12940650	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs6041736	chr20:12940650-12940651	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs552900996	chr20:12940711-12940712	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs555975669	chr20:12940720-12940721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs572160962	chr20:12940721-12940722	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs544836367	chr20:12940734-12940735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs113761819	chr20:12940736-12940737	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs6109628	chr20:12940737-12940738	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs192985768	chr20:12940767-12940768	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs71188132	chr20:12940768-12940769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs56260827	chr20:12940771-12940772	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs558128363	chr20:12940863-12940864	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs6105004	chr20:12940915-12940916	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs541148908	chr20:12940942-12940943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs142905485	chr20:12940970-12940971	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs564104562	chr20:12941026-12941027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs6134731	chr20:12941050-12941051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs374419297	chr20:12941086-12941087	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs375879879	chr20:12941159-12941160	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs77272035	chr20:12941193-12941194	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs560577605	chr20:12941210-12941211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs79374250	chr20:12941274-12941275	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs542682213	chr20:12941310-12941311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs562656109	chr20:12941327-12941328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs531362054	chr20:12941396-12941397	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs551556327	chr20:12941405-12941406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs33945145	chr20:12941407-12941408	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs397806340	chr20:12941418-12941419	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs6109629	chr20:12941450-12941451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs571446291	chr20:12941478-12941479	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs184316152	chr20:12941550-12941551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs547061753	chr20:12941554-12941555	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs111341301	chr20:12941569-12941570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs567298590	chr20:12941584-12941585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs372890694	chr20:12941597-12941598	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs539709252	chr20:12941637-12941638	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs536276333	chr20:12941653-12941654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs78839764	chr20:12941679-12941680	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs529452783	chr20:12941694-12941695	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs6041737	chr20:12941696-12941697	Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
50	rs538397611	chr20:12941703-12941704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

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
Autism	22102821	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12937200-12946000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:12942200-12942800	Enhancers	A549	lung
3	chr20:12942800-12949200	Weak transcription	A549	lung
4	chr20:12943000-12943200	Enhancers	Fetal Kidney	kidney
5	chr20:12943000-12947400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr20:12943200-12943800	Weak transcription	Fetal Kidney	kidney
7	chr20:12943600-12944200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:12943600-12944600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr20:12943600-12945800	Enhancers	Thymus	Thymus
10	chr20:12943800-12944600	Enhancers	Fetal Kidney	kidney
11	chr20:12944000-12944200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:12944000-12944200	Enhancers	Fetal Thymus	thymus
13	chr20:12944000-12944400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr20:12944000-12944400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:12944200-12944600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr20:12944400-12945400	Weak transcription	Fetal Thymus	thymus
17	chr20:12944400-12946000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:12944600-12946200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr20:12945400-12948400	Enhancers	Fetal Thymus	thymus
20	chr20:12945600-12946600	Enhancers	Brain Hippocampus Middle	brain
21	chr20:12945600-12946800	Enhancers	Brain Anterior Caudate	brain
22	chr20:12945600-12947800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr20:12945800-12946200	Enhancers	HUVEC	blood vessel
24	chr20:12945800-12946400	Flanking Active TSS	Thymus	Thymus
25	chr20:12945800-12946600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr20:12945800-12946800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr20:12946000-12946400	Enhancers	HSMM	muscle
28	chr20:12946000-12946600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr20:12946000-12946800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:12946000-12946800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:12946000-12946800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr20:12946000-12946800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr20:12946000-12946800	Enhancers	Brain Cingulate Gyrus	brain
34	chr20:12946000-12947000	Enhancers	Brain Substantia Nigra	brain
35	chr20:12946000-12947200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr20:12946200-12946600	Enhancers	Brain Germinal Matrix	brain
37	chr20:12946200-12946600	Enhancers	Fetal Muscle Leg	muscle
38	chr20:12946200-12947000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr20:12946200-12947000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr20:12946200-12947200	Enhancers	Primary T cells from cord blood	blood
41	chr20:12946200-12948000	Enhancers	Fetal Brain Male	brain
42	chr20:12946400-12946800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr20:12946400-12947000	Enhancers	HepG2	liver
44	chr20:12946400-12947400	Active TSS	Thymus	Thymus
45	chr20:12946600-12946800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr20:12947000-12947400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr20:12947000-12947400	Weak transcription	HepG2	liver
48	chr20:12947400-12947600	Enhancers	HepG2	liver
49	chr20:12947400-12947800	Enhancers	Fetal Brain Female	brain
50	chr20:12947400-12949600	Enhancers	Thymus	Thymus

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