Variant report

Variant	esv3410494
Chromosome Location	chr17:45212866-45213121
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	chr17:45211653..45214560-chr17:45231641..45234372,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYL4-2	chr17:45212171-45213246	ENSG00000249938

Variant related genes	Relation type
ENSG00000004897	chromatin interactions
BCCIP	miRNA target sites

Extended variants
information (count: 36 )
Associated
traits (count: 118 )

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200272570	chr17:45212877-45212878	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs75284424	chr17:45212878-45212879	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs77657363	chr17:45212879-45212880	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs375811852	chr17:45212885-45212886	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs62075598	chr17:45212892-45212893	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs55841275	chr17:45212898-45212899	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs548695905	chr17:45212911-45212912	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs62075599	chr17:45212913-45212914	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs199660984	chr17:45212926-45212927	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs62075600	chr17:45212927-45212928	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs62075601	chr17:45212950-45212951	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs565656902	chr17:45212963-45212964	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs537488558	chr17:45212965-45212966	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs557626874	chr17:45212966-45212967	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs571212472	chr17:45212971-45212972	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs79329544	chr17:45212976-45212977	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs79161705	chr17:45212977-45212978	ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs201495927	chr17:45213001-45213002	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs62075602	chr17:45213004-45213005	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs201714005	chr17:45213015-45213016	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs533709313	chr17:45213016-45213017	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs62075603	chr17:45213027-45213028	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs200232067	chr17:45213030-45213031	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs62075604	chr17:45213032-45213033	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs199718821	chr17:45213035-45213036	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs62075605	chr17:45213047-45213048	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs76561718	chr17:45213051-45213052	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs377099882	chr17:45213070-45213071	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs139390207	chr17:45213071-45213072	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs74596521	chr17:45213075-45213076	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs79621013	chr17:45213076-45213077	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs200340830	chr17:45213078-45213079	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs62075606	chr17:45213088-45213089	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs76718177	chr17:45213095-45213096	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs183165362	chr17:45213096-45213097	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs62075607	chr17:45213110-45213111	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:118)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Ovarian cancer	22174824	CNVD
Melanoma	18172304	CNVD
Moyamoya disease	22323933	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ovarian cancer	21781307	CNVD
Colorectal cancer	21645411	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell lymphomas	19863542	CNVD
Cancer	16751803	CNVD
Chordoma	21602918	CNVD
Neurofibromatosis	20686819	CNVD
Peripheral nerve sheath tumors	20686819	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Neuroblastoma	18923524	CNVD
Neuroblastoma	17897457	CNVD
Neuroblastoma	17327916	CNVD
Breast cancer	21264507	CNVD
Endometrial cancer	22040021	CNVD
Neuroblastoma	21484798	CNVD
Breast cancer	22028636	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute myeloid leukemia	20724749	CNVD
Breast cancer	21858162	CNVD
lymphocytic leukemia	21291569	CNVD
Gastric cancer	17167181	CNVD
Breast cancer	19287154	CNVD
Leukemia	20874852	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Neuroblastoma	18664255	CNVD
Neuroblastoma	17533364	CNVD
Human rectal carcinomas	16397240	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Breast cancer	17457667	CNVD
Breast cancer	16951389	CNVD
Basal cell lymphoma	17053054	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22048815	CNVD
Breast cancer	17603634	CNVD
Follicular lymphoma	20505157	CNVD
Non-small cell lung cancer	20864512	CNVD
Cancer	21183584	CNVD
Cervical cancer	21062161	CNVD
Breast cancer	20953835	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
TAR Syndrome	17847015	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17850661	CNVD
Breast cancer	19261255	CNVD
Lung cancer	16773561	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Basal-like breast cancer	18066063	CNVD
Breast cancer	20031965	CNVD
Colorectal cancer	19287155	CNVD
Hereditary breast	19566914	CNVD
Ovarian cancer	19047089	CNVD
Ovarian cancer	19566914	CNVD
Triple-negative breast cancer	18950515	CNVD
Breast cancer	16846527	CNVD
Bladder cancer	21909424	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	21251322	CNVD
Ewing''s sarcoma	22429812	CNVD
Prostate cancer	18632612	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Adenoid cystic carcinoma	18332873	CNVD
Breast cancer	17142309	CNVD
Breast cancer	16397240	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Myelofibrosis	22110671	CNVD
Prostate cancer	17217626	CNVD
Non-syndromic sensorineural hearing loss	21084979	CNVD
Autism	22817714	CNVD
Breast cancer	20409316	CNVD
Cancer	17160897	CNVD
Frontotemporal lobar degeneration	19640594	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Ovarian clear cell carcinoma	21343371	CNVD

Chromatin state (count:134 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45194800-45214400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:45194800-45234200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:45196600-45213000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:45196600-45213000	Weak transcription	Esophagus	oesophagus
5	chr17:45203800-45213000	Weak transcription	Right Ventricle	heart
6	chr17:45206400-45215200	Weak transcription	Brain Germinal Matrix	brain
7	chr17:45209600-45213000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:45209600-45213000	Weak transcription	Liver	Liver
9	chr17:45209600-45213000	Weak transcription	Placenta	Placenta
10	chr17:45210400-45218600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr17:45211200-45213200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr17:45212200-45213000	Weak transcription	Fetal Intestine Small	intestine
13	chr17:45212600-45214600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr17:45212600-45214600	Weak transcription	Fetal Brain Female	brain
15	chr17:45212600-45214800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr17:45212800-45213000	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:45212800-45213000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
18	chr17:45212800-45213000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
19	chr17:45212800-45213000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
20	chr17:45212800-45213000	Bivalent Enhancer	Brain Angular Gyrus	brain
21	chr17:45212800-45213200	ZNF genes & repeats	ES-WA7 Cell Line	embryonic stem cell
22	chr17:45212800-45213200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
23	chr17:45212800-45213200	Active TSS	Aorta	Aorta
24	chr17:45212800-45213200	ZNF genes & repeats	Brain Substantia Nigra	brain
25	chr17:45212800-45213200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
26	chr17:45212800-45213200	Flanking Bivalent TSS/Enh	A549	lung
27	chr17:45212800-45213200	ZNF genes & repeats	K562	blood
28	chr17:45212800-45213400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:45212800-45213400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
30	chr17:45212800-45213400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:45212800-45213400	ZNF genes & repeats	Fetal Thymus	thymus
32	chr17:45212800-45213400	ZNF genes & repeats	NHDF-Ad	bronchial
33	chr17:45212800-45213400	ZNF genes & repeats	NHLF	lung
34	chr17:45212800-45213400	ZNF genes & repeats	Osteobl	bone
35	chr17:45212800-45214800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
36	chr17:45212800-45214800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
37	chr17:45212800-45214800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr17:45212800-45214800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:45212800-45214800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
40	chr17:45212800-45214800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr17:45212800-45214800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:45212800-45214800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
43	chr17:45212800-45214800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
44	chr17:45212800-45214800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr17:45212800-45214800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:45212800-45214800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
47	chr17:45212800-45214800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
48	chr17:45212800-45214800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
49	chr17:45212800-45214800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr17:45212800-45214800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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