Variant report

Variant	nsv528393
Chromosome Location	chr7:79964962-79969058
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	chr7:79946374..79948233-chr7:79968387..79970856,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNAT3-1	chr7:79968064-79968243	ENSG00000232667.5

Variant related genes	Relation type
ENSG00000240347	chromatin interactions

Extended variants
information (count: 165 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:165 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6467113	chr7:79964962-79964963	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs112924636	chr7:79964966-79964967	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs79189601	chr7:79964985-79964986	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs565899324	chr7:79964993-79964994	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs191714166	chr7:79964997-79964998	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs548229546	chr7:79965011-79965012	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs562496563	chr7:79965031-79965032	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs531554782	chr7:79965073-79965074	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs142195551	chr7:79965075-79965076	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs537451135	chr7:79965095-79965096	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs556213281	chr7:79965109-79965110	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs544939950	chr7:79965202-79965203	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs372060944	chr7:79965229-79965230	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs576271625	chr7:79965238-79965239	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs114229085	chr7:79965239-79965240	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs375231376	chr7:79965261-79965262	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs558807903	chr7:79965307-79965308	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs572222641	chr7:79965324-79965325	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs78146113	chr7:79965329-79965330	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs560952773	chr7:79965330-79965331	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs183935023	chr7:79965357-79965358	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs538760942	chr7:79965376-79965377	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs374110475	chr7:79965379-79965380	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs188882779	chr7:79965454-79965455	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs145803033	chr7:79965461-79965462	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs117849929	chr7:79965473-79965474	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs552568157	chr7:79965474-79965475	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs191440946	chr7:79965486-79965487	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs528622258	chr7:79965520-79965521	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs115119780	chr7:79965566-79965567	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs182476366	chr7:79965579-79965580	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs527280877	chr7:79965587-79965588	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs376347269	chr7:79965589-79965590	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs537084735	chr7:79965613-79965614	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs186754563	chr7:79965630-79965631	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs147997470	chr7:79965685-79965686	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs538925914	chr7:79965708-79965709	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs558848356	chr7:79965752-79965753	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs572307384	chr7:79965757-79965758	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs534810763	chr7:79965777-79965778	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs141690863	chr7:79965784-79965785	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs535761986	chr7:79965789-79965790	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs547457550	chr7:79965874-79965875	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs543119270	chr7:79965887-79965888	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs556940219	chr7:79965888-79965889	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs369615462	chr7:79966011-79966012	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs191888643	chr7:79966012-79966013	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs184809356	chr7:79966016-79966017	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs567280101	chr7:79966034-79966035	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs528688691	chr7:79966058-79966059	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Basal cell lymphoma	17170743	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Seminomas	18059402	CNVD
Testicular cancer	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	19415332	CNVD
Medulloblastoma	21979893	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
T-cell lymphomas	19863542	CNVD
Malaria	21533027	CNVD
Melanoma	18172304	CNVD
Renal cell carcinoma	19461508	CNVD
head and neck squamous cell carcinoma	19289630	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Biliary cancer	19435499	CNVD
Multiple myeloma	16461302	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Hepatocellular carcinoma	16750200	CNVD
Non-small cell lung cancer	21829676	CNVD
Gastric cancer	24379144	CNVD
Glioblastoma multiforme	17002787	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lissencephaly	21572526	CNVD
Breast cancer	17603634	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	16397240	CNVD
Acute myeloid leukemia	16864856	CNVD
Squamous cell cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	17387387	CNVD
Low-grade fibromyxoid sarcoma	0	CNVD
Oligodendroglial tumors	17285580	CNVD
Endometrial cancer	22040021	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	21264507	CNVD
Shwachman-Diamond syndrome	22934832	CNVD
Colorectal cancer	19359472	CNVD
Cutaneous malignant melanoma	17690212	CNVD
Leukemia	17361228	CNVD
Breast cancer	16461572	CNVD
Peripheral t-cell lymphoma	19118030	CNVD
Malignant melanoma	17690212	CNVD
Renal cell carcinoma	18592004	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Neurodevelopmental disorder	22521361	CNVD
Williams Syndrome	20824207	CNVD
Metanephric adenoma	20802469	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
abortions and stillbirths	19751515	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	21364760	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Williams-beuren syndrome	16826523	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	19318497	CNVD
Multiple myeloma	16616336	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Schizophrenia	17879154	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	16461572	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Autism	20858243	CNVD
Cancer	20164919	CNVD
Breast cancer	21611746	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79954200-79975400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:79962800-79965600	Enhancers	Fetal Intestine Large	intestine
3	chr7:79963000-79966200	Enhancers	Fetal Intestine Small	intestine
4	chr7:79963200-79965000	Enhancers	Duodenum Mucosa	Duodenum
5	chr7:79963200-79965000	Enhancers	Small Intestine	intestine
6	chr7:79963400-79965200	Enhancers	Fetal Kidney	kidney
7	chr7:79963400-79965400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:79963400-79965600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr7:79963400-79966200	Enhancers	Primary hematopoietic stem cells	blood
10	chr7:79963600-79965400	Enhancers	Fetal Muscle Leg	muscle
11	chr7:79963600-79965400	Enhancers	Stomach Mucosa	stomach
12	chr7:79963800-79965400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:79963800-79965400	Enhancers	Adipose Nuclei	Adipose
14	chr7:79964000-79965200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr7:79964000-79965400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr7:79964200-79965200	Enhancers	Fetal Stomach	stomach
17	chr7:79964200-79965400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:79964200-79965400	Enhancers	Liver	Liver
19	chr7:79964200-79965400	Enhancers	HUVEC	blood vessel
20	chr7:79964200-79965600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:79964400-79965000	Enhancers	Brain Substantia Nigra	brain
22	chr7:79964400-79965200	Enhancers	Colon Smooth Muscle	Colon
23	chr7:79964400-79965200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr7:79964400-79965400	Enhancers	Fetal Lung	lung
25	chr7:79964800-79965000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:79964800-79965000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:79964800-79965000	Active TSS	Brain Hippocampus Middle	brain
28	chr7:79964800-79965000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr7:79964800-79965000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr7:79964800-79965000	Active TSS	HSMMtube	muscle
31	chr7:79964800-79965200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:79964800-79965200	Flanking Active TSS	Brain Cingulate Gyrus	brain
33	chr7:79964800-79965200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr7:79964800-79965400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:79964800-79965400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr7:79964800-79965400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr7:79964800-79965400	Enhancers	Brain Anterior Caudate	brain
38	chr7:79964800-79965400	Enhancers	Gastric	stomach
39	chr7:79964800-79965400	Enhancers	Left Ventricle	heart
40	chr7:79964800-79965400	Enhancers	Ovary	ovary
41	chr7:79964800-79965400	Enhancers	Pancreas	Pancrea
42	chr7:79964800-79965400	Enhancers	Right Atrium	heart
43	chr7:79964800-79965400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr7:79964800-79965400	Flanking Active TSS	HSMM	muscle
45	chr7:79964800-79965600	Enhancers	Aorta	Aorta
46	chr7:79964800-79965600	Enhancers	Brain Angular Gyrus	brain
47	chr7:79965000-79965200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:79965000-79965200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:79965000-79965200	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr7:79965000-79965200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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