Variant report

Variant	esv3470852
Chromosome Location	chr11:66303930-66305318
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66302009..66305192-chr11:66317056..66320691,3	MCF-7	breast:
2	chr11:66302822..66304385-chr11:66311282..66313509,2	K562	blood:
3	chr11:66304927..66310447-chr11:66310654..66314937,8	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTSF-2	chr11:66303369-66305407	ENSG00000269990.1

Variant related genes	Relation type
ENSG00000174165	chromatin interactions
ENSG00000248746	chromatin interactions

Extended variants
information (count: 75 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:75 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs186470676	chr11:66303942-66303943	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs113925446	chr11:66303969-66303970	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs571038156	chr11:66303972-66303973	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs376542174	chr11:66303979-66303980	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs530687504	chr11:66304008-66304009	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs559329166	chr11:66304020-66304021	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs190503299	chr11:66304069-66304070	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs545603022	chr11:66304080-66304081	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs138183900	chr11:66304093-66304094	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs539615916	chr11:66304138-66304139	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs550323957	chr11:66304141-66304142	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs546713625	chr11:66304143-66304144	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs183112279	chr11:66304203-66304204	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs535555391	chr11:66304237-66304238	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs548676497	chr11:66304238-66304239	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs568865321	chr11:66304270-66304271	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs570147412	chr11:66304277-66304278	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs573040806	chr11:66304317-66304318	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs200722508	chr11:66304424-66304425	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs112704677	chr11:66304432-66304433	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs557272982	chr11:66304435-66304436	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs563994468	chr11:66304502-66304503	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs539599084	chr11:66304516-66304517	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs187915299	chr11:66304525-66304526	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs572967205	chr11:66304559-66304560	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs542330831	chr11:66304615-66304616	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs115072816	chr11:66304628-66304629	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs575626164	chr11:66304644-66304645	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs373705807	chr11:66304654-66304655	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs149167903	chr11:66304697-66304698	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs564417866	chr11:66304698-66304699	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs191583786	chr11:66304721-66304722	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs540396445	chr11:66304738-66304739	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs560413219	chr11:66304784-66304785	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs528959644	chr11:66304806-66304807	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs59213528	chr11:66304808-66304809	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs145445126	chr11:66304813-66304814	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs531386624	chr11:66304864-66304865	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs550967647	chr11:66304872-66304873	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs182555005	chr11:66304885-66304886	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs112732820	chr11:66304914-66304915	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs553121058	chr11:66304915-66304916	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs567078870	chr11:66304927-66304928	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs535562614	chr11:66304930-66304931	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
45	rs555795535	chr11:66304951-66304952	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
46	rs555870265	chr11:66305024-66305025	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
47	rs79845838	chr11:66305029-66305030	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
48	rs575955832	chr11:66305033-66305034	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
49	rs187689376	chr11:66305034-66305035	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
50	rs577978915	chr11:66305035-66305036	Weak transcription Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Multiple myeloma	20724749	CNVD
Wilms tumour	21544195	CNVD
Autism	22495311	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Non-small cell lung cancer	21385341	CNVD
Intellectual disability	22102821	CNVD
Glioblastoma multiforme	21138945	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	21637783	CNVD
Acute myeloid leukemia	16864856	CNVD
Chronic lymphocytic leukemia	21795749	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21484798	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	21386901	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	20837533	CNVD
Breast cancer	21264507	CNVD
Cervical cancer	21063398	CNVD
Glioblastoma multiforme	19960244	CNVD
Liposarcoma	21253554	CNVD
Neuroblastoma	18923524	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Neuroblastoma	17533364	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Prostate cancer	18632612	CNVD
Glioblastoma multiforme	21080181	CNVD
Smith-Lemli-Opitz syndrome	21572526	CNVD
Multiple myeloma	16461302	CNVD
Cancer	16751803	CNVD
Seminomas	18059402	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Metanephric adenoma	20802469	CNVD
Chordoma	21602918	CNVD
Melanoma	18172304	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
ovarian endometriomas	16273235	CNVD
Breast cancer	16417655	CNVD
Myelofibrosis	22110671	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	17217626	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Breast cancer	21045282	CNVD
Breast cancer	21806811	CNVD
Breast cancer	22002566	CNVD
Ductal carcinoma	18381933	CNVD
Retinoblastoma	22278416	CNVD
Breast cancer	20953835	CNVD
oto-dental syndrome	17656375	CNVD
Asthma	21956041	CNVD
Breast cancer	17603634	CNVD
Ovarian neoplasms	16753589	CNVD
Non-small cell lung cancer	20864512	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cervical cancer	21062161	CNVD
Breast cancer	21509527	CNVD
Breast cancer	17001317	CNVD
Oral squamous cell carcinoma	16619035	CNVD
Intracranial aneurysm	16715129	CNVD
Colorectal cancer	16272173	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Colorectal cancer	16882699	CNVD
Berardinelli-seip congenital generalized lipodystrophy	17668395	CNVD
Spinal muscular atrophy	17668395	CNVD
Neonatal seizures	17668395	CNVD
Neonatal seizures	17668391	CNVD
Neuroticism	17667963	CNVD
Cancer	17916600	CNVD
Squamous cell cancer	19047905	CNVD
Multiple endocrine neoplasia type 1	19566914	CNVD
XY sex reversal	17503084	CNVD
Berardinelli-seip congenital generalized lipodystrophy	17668391	CNVD
Maculopathy	17646752	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17157792	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Hodgkin''s lymphoma	17606441	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:172 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66278600-66311000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66278800-66309800	Weak transcription	HSMMtube	muscle
3	chr11:66278800-66312800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:66279000-66306200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:66279000-66309200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:66279000-66313000	Weak transcription	Small Intestine	intestine
7	chr11:66279200-66309800	Weak transcription	HUVEC	blood vessel
8	chr11:66279200-66310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:66279200-66310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:66279200-66310800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr11:66279400-66311000	Weak transcription	Fetal Brain Male	brain
12	chr11:66279400-66311200	Weak transcription	Right Atrium	heart
13	chr11:66279800-66305200	Strong transcription	Fetal Muscle Leg	muscle
14	chr11:66281000-66311000	Strong transcription	Fetal Stomach	stomach
15	chr11:66282000-66309600	Weak transcription	NHDF-Ad	bronchial
16	chr11:66283400-66312800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr11:66289000-66308200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:66289000-66309800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:66289000-66312800	Weak transcription	Stomach Mucosa	stomach
20	chr11:66290200-66310800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr11:66291000-66309800	Weak transcription	HSMM	muscle
22	chr11:66291200-66306200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:66291200-66309800	Weak transcription	NH-A	brain
24	chr11:66291200-66311600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:66291400-66304200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:66291400-66304400	Weak transcription	Psoas Muscle	Psoas
27	chr11:66291400-66305800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:66291400-66305800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:66291400-66309400	Weak transcription	A549	lung
30	chr11:66291400-66309600	Weak transcription	GM12878-XiMat	blood
31	chr11:66291400-66311000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:66291600-66306200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr11:66291600-66309200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr11:66291600-66309800	Weak transcription	HMEC	breast
35	chr11:66291600-66312600	Weak transcription	NHEK	skin
36	chr11:66292000-66306200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:66292000-66306200	Weak transcription	Dnd41	blood
38	chr11:66292000-66306600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:66292200-66304400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:66293200-66305200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:66293600-66311000	Strong transcription	Fetal Intestine Small	intestine
42	chr11:66293800-66305200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr11:66294600-66306200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:66294600-66306600	Weak transcription	NHLF	lung
45	chr11:66294600-66308800	Weak transcription	Brain Substantia Nigra	brain
46	chr11:66294800-66312400	Weak transcription	Hela-S3	cervix
47	chr11:66295400-66304600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:66295800-66306000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr11:66296200-66304000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:66296200-66304200	Weak transcription	Primary T cells fromperipheralblood	blood

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