Variant report

Variant	esv2260962
Chromosome Location	chr3:195671612-195672285
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFRC-1	chr3:195668449-195672581	NONHSAT094272

Extended variants
information (count: 65 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:65 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs199712128	chr3:195671612-195671613	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs186340174	chr3:195671621-195671622	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs569084389	chr3:195671640-195671641	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs370549938	chr3:195671643-195671644	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs536495009	chr3:195671656-195671657	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs548341453	chr3:195671681-195671682	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs9878111	chr3:195671682-195671683	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs372213727	chr3:195671699-195671700	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs534055865	chr3:195671705-195671706	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs558289835	chr3:195671710-195671711	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs190751199	chr3:195671725-195671726	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs4927802	chr3:195671728-195671729	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs555879219	chr3:195671730-195671731	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs11707529	chr3:195671735-195671736	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs111908821	chr3:195671738-195671739	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs542087545	chr3:195671752-195671753	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs554327670	chr3:195671761-195671762	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs572665953	chr3:195671774-195671775	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs546451078	chr3:195671775-195671776	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs372313194	chr3:195671776-195671777	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs184649699	chr3:195671814-195671815	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs531699051	chr3:195671835-195671836	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs543833254	chr3:195671836-195671837	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs375596367	chr3:195671837-195671838	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs187996547	chr3:195671841-195671842	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs529387462	chr3:195671844-195671845	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs548096477	chr3:195671845-195671846	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs566631815	chr3:195671847-195671848	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs11709120	chr3:195671861-195671862	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	mRNA abundance
30	rs187466813	chr3:195671868-195671869	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	mRNA abundance
31	rs201102084	chr3:195671884-195671885	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs12488898	chr3:195671894-195671895	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs376510765	chr3:195671913-195671914	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs12486840	chr3:195671926-195671927	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs376798575	chr3:195671931-195671932	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs12486841	chr3:195671934-195671935	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs570402836	chr3:195671964-195671965	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs537496609	chr3:195671965-195671966	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs112066117	chr3:195671983-195671984	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs200119817	chr3:195671988-195671989	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs555719614	chr3:195672001-195672002	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs12497208	chr3:195672011-195672012	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs368976003	chr3:195672020-195672021	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs200996305	chr3:195672025-195672026	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs62285286	chr3:195672035-195672036	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs552722418	chr3:195672038-195672039	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs112518575	chr3:195672047-195672048	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs61645273	chr3:195672101-195672102	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs56150637	chr3:195672104-195672105	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs190996347	chr3:195672106-195672107	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195647200-195681200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:195648600-195680600	Weak transcription	Pancreas	Pancrea
3	chr3:195651800-195673800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:195656600-195681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:195656800-195676400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:195656800-195679400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:195657800-195681400	Weak transcription	GM12878-XiMat	blood
8	chr3:195659000-195676400	Weak transcription	Hela-S3	cervix
9	chr3:195659600-195681200	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:195659600-195685600	Weak transcription	Small Intestine	intestine
11	chr3:195660000-195681200	Weak transcription	Colonic Mucosa	Colon
12	chr3:195660400-195680600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:195660600-195681200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:195661200-195681000	Weak transcription	Ovary	ovary
15	chr3:195661800-195681200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:195663400-195681200	Weak transcription	Left Ventricle	heart
17	chr3:195663600-195673800	Weak transcription	Liver	Liver
18	chr3:195663600-195681000	Weak transcription	Fetal Brain Female	brain
19	chr3:195663600-195681200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:195663600-195681200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:195663800-195682000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:195664400-195681200	Weak transcription	Osteobl	bone
23	chr3:195665000-195681200	Weak transcription	Placenta	Placenta
24	chr3:195665200-195677800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:195665200-195691800	Weak transcription	HSMMtube	muscle
26	chr3:195665400-195681400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:195665400-195685200	Weak transcription	Aorta	Aorta
28	chr3:195666000-195673200	Weak transcription	Primary B cells from cord blood	blood
29	chr3:195666000-195677200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:195666000-195677800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:195667200-195681200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:195667400-195677200	Weak transcription	Gastric	stomach
33	chr3:195667400-195677200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:195667400-195680800	Weak transcription	Right Ventricle	heart
35	chr3:195667400-195681200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:195667400-195681200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:195667400-195681200	Weak transcription	Brain Anterior Caudate	brain
38	chr3:195667400-195681200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:195667400-195681200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:195667400-195681200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:195667400-195681400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:195667400-195681400	Weak transcription	Brain Substantia Nigra	brain
43	chr3:195667400-195684200	Weak transcription	Spleen	Spleen
44	chr3:195667400-195686200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:195667600-195677600	Weak transcription	Primary T cells from cord blood	blood
46	chr3:195667600-195680200	Weak transcription	Fetal Stomach	stomach
47	chr3:195667600-195681200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:195667600-195681200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:195667600-195681200	Weak transcription	Esophagus	oesophagus
50	chr3:195667600-195681400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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