Variant report

Variant	esv2443936
Chromosome Location	chr1:246927638-246929072
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	chr1:246922007..246925353-chr1:246926619..246930863,4	K562	blood:
2	chr1:246860479..246862658-chr1:246926455..246929333,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNST-3	chr1:246928783-246929034	NONHSAT010721

Extended variants
information (count: 49 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:49 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs369539498	chr1:246927669-246927670	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs570299524	chr1:246927710-246927711	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs184190045	chr1:246927735-246927736	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs567611525	chr1:246927736-246927737	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs572582947	chr1:246927779-246927780	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs534792305	chr1:246927811-246927812	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs557871825	chr1:246927824-246927825	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs146600646	chr1:246927858-246927859	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs543366665	chr1:246927866-246927867	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs563364834	chr1:246927918-246927919	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs188123086	chr1:246927998-246927999	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs542583162	chr1:246927999-246928000	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs559495880	chr1:246928031-246928032	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs567709130	chr1:246928033-246928034	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs373583584	chr1:246928051-246928052	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs181014907	chr1:246928055-246928056	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs535405531	chr1:246928062-246928063	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs564923931	chr1:246928108-246928109	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs116381224	chr1:246928127-246928128	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs550558179	chr1:246928168-246928169	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs113854730	chr1:246928210-246928211	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs567186778	chr1:246928212-246928213	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs56289899	chr1:246928216-246928217	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs60666824	chr1:246928232-246928233	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs55725131	chr1:246928235-246928236	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs542037473	chr1:246928275-246928276	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs61057914	chr1:246928276-246928277	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs536126476	chr1:246928278-246928279	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs565795994	chr1:246928323-246928324	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs549461310	chr1:246928355-246928356	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs539636964	chr1:246928362-246928363	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs368150918	chr1:246928364-246928365	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs10924819	chr1:246928408-246928409	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs66546675	chr1:246928425-246928426	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs113103973	chr1:246928452-246928453	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs10924820	chr1:246928540-246928541	Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
37	rs185674057	chr1:246928558-246928559	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs557933726	chr1:246928605-246928606	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs571380333	chr1:246928639-246928640	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs4244625	chr1:246928676-246928677	Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs557301080	chr1:246928695-246928696	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs573996558	chr1:246928765-246928766	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs138527970	chr1:246928801-246928802	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs368371757	chr1:246928812-246928813	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs371833931	chr1:246928867-246928868	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs376733880	chr1:246928932-246928933	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs115043452	chr1:246928982-246928983	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs149236918	chr1:246928991-246928992	Weak transcription Strong transcription Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs4926440	chr1:246929018-246929019	Weak transcription Strong transcription Genic enhancers Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:83)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Melanoma	18172304	CNVD
Medulloblastoma	21979893	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Neuroblastoma	21899760	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	20729466	CNVD
Testicular germ cell tumor	18059402	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-small cell lung cancer	21829676	CNVD
Multiple myeloma	16616336	CNVD
Ovarian cancer	21720365	CNVD
Glioblastoma multiforme	22291905	CNVD
Myelofibrosis	22110671	CNVD
Disease	21936942	CNVD
laryngomalacia	21936942	CNVD
GLUT3 deficiency syndrome	20509907	CNVD
Developmental delay	21373258	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Developmental delay	19490664	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Cutaneous malignant melanoma	18794153	CNVD
Astrocytoma	17934521	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Breast cancer	20409316	CNVD
Fibroblasts	17951408	CNVD
Lung cancer	17951408	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246888400-246946400	Weak transcription	Small Intestine	intestine
2	chr1:246888600-246945600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:246889000-246929000	Weak transcription	Stomach Mucosa	stomach
4	chr1:246895000-246942200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:246895400-246938600	Weak transcription	Fetal Heart	heart
6	chr1:246902800-246952800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:246904600-246942800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:246905000-246945800	Weak transcription	Psoas Muscle	Psoas
9	chr1:246905800-246931600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:246912600-246930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:246912600-246932200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:246912800-246933200	Weak transcription	K562	blood
13	chr1:246917600-246931000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:246917600-246931200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:246917600-246936000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:246917800-246930800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:246918000-246930200	Weak transcription	Right Ventricle	heart
18	chr1:246920800-246931200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:246920800-246944200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:246921000-246931800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:246921200-246943200	Strong transcription	Dnd41	blood
22	chr1:246921600-246945800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:246922000-246929800	Strong transcription	Fetal Thymus	thymus
24	chr1:246922000-246932000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:246922000-246936400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:246922200-246928400	Strong transcription	HSMMtube	muscle
27	chr1:246922200-246930400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:246922200-246931200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:246922200-246931200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:246922200-246932200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:246922200-246932800	Strong transcription	HepG2	liver
32	chr1:246922200-246933000	Strong transcription	Fetal Intestine Large	intestine
33	chr1:246922200-246934400	Strong transcription	Placenta	Placenta
34	chr1:246922200-246936000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:246922200-246936000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:246922200-246936200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:246922200-246937000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:246922200-246944600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:246922400-246929600	Strong transcription	Brain Anterior Caudate	brain
40	chr1:246922400-246932200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:246922600-246930000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:246922600-246936400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:246922800-246932000	Strong transcription	Osteobl	bone
44	chr1:246923000-246929400	Strong transcription	HSMM	muscle
45	chr1:246923000-246931000	Strong transcription	HUVEC	blood vessel
46	chr1:246923000-246932200	Strong transcription	Adipose Nuclei	Adipose
47	chr1:246923000-246933000	Strong transcription	Primary T cells from cord blood	blood
48	chr1:246923000-246936200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr1:246923200-246945000	Strong transcription	Fetal Muscle Leg	muscle
50	chr1:246923400-246932600	Strong transcription	Skeletal Muscle Male	skeletal muscle

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