Variant report

Variant	esv12124
Chromosome Location	chr15:73659979-73661419
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	chr15:73659851..73663146-chr15:73925069..73927598,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPTN-2	chr15:73660613-73661255	NONHSAT047146

Variant related genes	Relation type
ENSG00000156642	chromatin interactions

Extended variants
information (count: 29 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs545040345	chr15:73659979-73659980	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs200186692	chr15:73660025-73660026	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs201375192	chr15:73660028-73660029	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs375206856	chr15:73660051-73660052	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs571671463	chr15:73660066-73660067	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs111892410	chr15:73660078-73660079	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs369418464	chr15:73660084-73660085	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs542532555	chr15:73660092-73660093	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs560874115	chr15:73660154-73660155	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs531489450	chr15:73660167-73660168	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs549753996	chr15:73660355-73660356	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs143090627	chr15:73660505-73660506	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs376849038	chr15:73660564-73660565	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs201193660	chr15:73660576-73660577	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs547829940	chr15:73660645-73660646	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs566095713	chr15:73660741-73660742	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs536621293	chr15:73660781-73660782	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs548581131	chr15:73660800-73660801	Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs577671006	chr15:73660879-73660880	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs183675842	chr15:73661018-73661019	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs537745479	chr15:73661047-73661048	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs146150604	chr15:73661109-73661110	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs577325559	chr15:73661158-73661159	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs188896349	chr15:73661179-73661180	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs538368084	chr15:73661193-73661194	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs140161530	chr15:73661196-73661197	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs536533926	chr15:73661297-73661298	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs571784371	chr15:73661303-73661304	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs556778812	chr15:73661350-73661351	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Wilms tumour	21544195	CNVD
Testicular germ cell tumor	18059402	CNVD
cataract	16735990	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Medulloblastoma	21979893	CNVD
spastic paraplegia with thinning of corpus callosum	19105190	CNVD
Schizophrenia	21324950	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Disease	21824424	CNVD
Melanoma	18172304	CNVD
Gastric cancer	17167181	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Colorectal cancer	16272173	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Multiple myeloma	17550852	CNVD
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Lung cancer	18438408	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Cancer	16751803	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	17133270	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Prostate cancer	16573809	CNVD
Autism	17322880	CNVD
phobic disorder	16773131	CNVD
Autism	21480499	CNVD
Disorders of sex development	22290220	CNVD
Mental retardation	19951919	CNVD
Mental retardation	16773131	CNVD
T-cell lymphomas	19863542	CNVD
15q24 microdeletion syndrome	22180641	CNVD
15q24 microdeletion syndrome	19921647	CNVD
Disease	22216833	CNVD
Mental retardation	17360722	CNVD
15q24 microdeletion syndrome	22216833	CNVD
15q24 microdeletion syndrome	22283845	CNVD
Developmental delay	17932688	CNVD
craniofacial dysmorphism	17932688	CNVD
digital and genital abnormalities	17932688	CNVD
Mental retardation	17621639	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Epilepsy	22083797	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	20067559	CNVD

Chromatin state (count:210 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73658600-73660000	Active TSS	Fetal Heart	heart
2	chr15:73658600-73661800	Active TSS	Right Atrium	heart
3	chr15:73658800-73660000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
4	chr15:73658800-73660000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:73659000-73660000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
6	chr15:73659000-73660000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:73659000-73660600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:73659200-73660000	Bivalent Enhancer	Placenta	Placenta
9	chr15:73659200-73660600	Bivalent Enhancer	Lung	lung
10	chr15:73659200-73661400	Active TSS	Left Ventricle	heart
11	chr15:73659200-73661600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr15:73659200-73661800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
13	chr15:73659200-73662000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:73659400-73660000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:73659400-73660000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
16	chr15:73659400-73660000	Bivalent Enhancer	Fetal Intestine Large	intestine
17	chr15:73659400-73660000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr15:73659400-73661200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
19	chr15:73659400-73661400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr15:73659400-73661800	Bivalent Enhancer	Spleen	Spleen
21	chr15:73659400-73662000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:73659400-73662000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr15:73659400-73662200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr15:73659400-73662200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
25	chr15:73659600-73660000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
26	chr15:73659600-73660000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:73659600-73660000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:73659600-73660000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:73659600-73660000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
30	chr15:73659600-73660000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
31	chr15:73659600-73660200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
32	chr15:73659600-73660200	Bivalent Enhancer	Brain Hippocampus Middle	brain
33	chr15:73659600-73661400	Flanking Active TSS	Pancreas	Pancrea
34	chr15:73659600-73661800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:73659600-73662200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr15:73659600-73662200	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr15:73659800-73660000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr15:73659800-73660000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:73659800-73660000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
40	chr15:73659800-73660000	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
41	chr15:73659800-73660000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
42	chr15:73659800-73660000	Bivalent Enhancer	Fetal Stomach	stomach
43	chr15:73659800-73660000	Active TSS	Right Ventricle	heart
44	chr15:73659800-73660000	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr15:73659800-73660000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr15:73659800-73660200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:73659800-73660200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:73659800-73660200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:73659800-73660200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:73659800-73660200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum

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