Variant report

Variant	esv3435306
Chromosome Location	chr3:195669155-195674053
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	chr3:195673861..195675995-chr5:278201..279705,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFRC-1	chr3:195668449-195672581	NONHSAT094272
2	lnc-TNK2-2	chr3:195673684-195674350	NONHSAT094275

Extended variants
information (count: 369 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:369 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs150363417	chr3:195669175-195669176	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs62284426	chr3:195669198-195669199	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs533284008	chr3:195669230-195669231	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs545459034	chr3:195669233-195669234	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs564132524	chr3:195669240-195669241	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs76806348	chr3:195669245-195669246	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs2933385	chr3:195669246-195669247	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs531365887	chr3:195669256-195669257	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs79242350	chr3:195669282-195669283	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs549556776	chr3:195669290-195669291	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs59274944	chr3:195669323-195669324	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs113785478	chr3:195669336-195669337	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs538654768	chr3:195669342-195669343	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs369845323	chr3:195669343-195669344	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs529131545	chr3:195669353-195669354	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs547025389	chr3:195669381-195669382	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs55874542	chr3:195669400-195669401	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs142189506	chr3:195669411-195669412	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs557792868	chr3:195669417-195669418	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs569640525	chr3:195669428-195669429	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs537686288	chr3:195669430-195669431	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs555973389	chr3:195669458-195669459	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs74622800	chr3:195669464-195669465	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs76934808	chr3:195669480-195669481	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs553115684	chr3:195669494-195669495	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs183509094	chr3:195669526-195669527	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs545184133	chr3:195669549-195669550	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs563845234	chr3:195669562-195669563	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs186578771	chr3:195669566-195669567	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs191825837	chr3:195669575-195669576	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs112655150	chr3:195669577-195669578	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs561530866	chr3:195669591-195669592	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs74778113	chr3:195669598-195669599	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs369689794	chr3:195669605-195669606	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs76106948	chr3:195669607-195669608	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs370534664	chr3:195669672-195669673	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs559095598	chr3:195669676-195669677	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs532984193	chr3:195669684-195669685	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs551083878	chr3:195669685-195669686	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs569792641	chr3:195669697-195669698	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs537126173	chr3:195669698-195669699	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs549613000	chr3:195669699-195669700	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs567833472	chr3:195669719-195669720	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs62284427	chr3:195669750-195669751	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs372623243	chr3:195669764-195669765	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs6805855	chr3:195669849-195669850	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs553592797	chr3:195669865-195669866	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs199522963	chr3:195669884-195669885	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs578182147	chr3:195669886-195669887	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs539073181	chr3:195669887-195669888	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:83)

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
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:151 , 50 per page) page: 1 2 3 4

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	chr3:195651200-195671200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:195651800-195673800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:195656600-195681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:195656800-195669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:195656800-195671200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:195656800-195676400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:195656800-195679400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:195657400-195670000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:195657800-195681400	Weak transcription	GM12878-XiMat	blood
12	chr3:195659000-195676400	Weak transcription	Hela-S3	cervix
13	chr3:195659600-195681200	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:195659600-195685600	Weak transcription	Small Intestine	intestine
15	chr3:195660000-195669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:195660000-195681200	Weak transcription	Colonic Mucosa	Colon
17	chr3:195660400-195680600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:195660600-195669600	Weak transcription	A549	lung
19	chr3:195660600-195681200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:195660800-195669400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:195661200-195681000	Weak transcription	Ovary	ovary
22	chr3:195661400-195669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:195661800-195669800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:195661800-195681200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:195663400-195681200	Weak transcription	Left Ventricle	heart
26	chr3:195663600-195673800	Weak transcription	Liver	Liver
27	chr3:195663600-195681000	Weak transcription	Fetal Brain Female	brain
28	chr3:195663600-195681200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:195663600-195681200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:195663800-195682000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:195664400-195681200	Weak transcription	Osteobl	bone
32	chr3:195665000-195681200	Weak transcription	Placenta	Placenta
33	chr3:195665200-195677800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:195665200-195691800	Weak transcription	HSMMtube	muscle
35	chr3:195665400-195681400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:195665400-195685200	Weak transcription	Aorta	Aorta
37	chr3:195666000-195673200	Weak transcription	Primary B cells from cord blood	blood
38	chr3:195666000-195677200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:195666000-195677800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:195666400-195670600	Strong transcription	Fetal Intestine Small	intestine
41	chr3:195666600-195669400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:195667200-195669400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:195667200-195681200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:195667400-195669800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:195667400-195671200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:195667400-195677200	Weak transcription	Gastric	stomach
47	chr3:195667400-195677200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:195667400-195680800	Weak transcription	Right Ventricle	heart
49	chr3:195667400-195681200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:195667400-195681200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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