Variant report

Variant	esv3388695
Chromosome Location	chr3:195688455-195692553
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNK2-6	chr3:195688656-195689069	expReg_chr3_13675_-

Extended variants
information (count: 311 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:311 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200948205	chr3:195688471-195688472	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs376232836	chr3:195688477-195688478	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs546467031	chr3:195688479-195688480	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs190989579	chr3:195688481-195688482	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs74491453	chr3:195688488-195688489	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs183177256	chr3:195688495-195688496	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs186789525	chr3:195688500-195688501	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs112676825	chr3:195688502-195688503	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs144267475	chr3:195688503-195688504	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs191276629	chr3:195688507-195688508	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs567718985	chr3:195688509-195688510	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs535827529	chr3:195688518-195688519	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs547907863	chr3:195688519-195688520	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs372768533	chr3:195688529-195688530	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs113186203	chr3:195688544-195688545	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs78376741	chr3:195688561-195688562	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs566222703	chr3:195688570-195688571	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs534415707	chr3:195688571-195688572	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs558841071	chr3:195688573-195688574	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs183024383	chr3:195688586-195688587	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs373776387	chr3:195688593-195688594	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs368553239	chr3:195688600-195688601	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs139977870	chr3:195688602-195688603	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs538121501	chr3:195688610-195688611	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs556881441	chr3:195688616-195688617	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs143435193	chr3:195688619-195688620	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	mRNA abundance
27	rs574916163	chr3:195688631-195688632	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs374236007	chr3:195688632-195688633	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs112840130	chr3:195688646-195688647	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs376324773	chr3:195688672-195688673	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs368663145	chr3:195688694-195688695	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs572407474	chr3:195688704-195688705	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs62282783	chr3:195688708-195688709	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs112081327	chr3:195688717-195688718	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs547596816	chr3:195688719-195688720	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs74709279	chr3:195688723-195688724	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs532450014	chr3:195688726-195688727	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs544211478	chr3:195688740-195688741	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs549324294	chr3:195688744-195688745	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs371494990	chr3:195688749-195688750	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs538915057	chr3:195688751-195688752	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs555274471	chr3:195688763-195688764	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs369507568	chr3:195688764-195688765	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs562419108	chr3:195688768-195688769	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs75277005	chr3:195688776-195688777	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs62282784	chr3:195688778-195688779	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs376627998	chr3:195688779-195688780	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs202220362	chr3:195688781-195688782	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs80061884	chr3:195688801-195688802	Weak transcription ZNF genes & repeats Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs373451629	chr3:195688806-195688807	Weak transcription ZNF genes & repeats Strong transcription Enhancers	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:323 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195665200-195691800	Weak transcription	HSMMtube	muscle
2	chr3:195677800-195691800	Weak transcription	NHDF-Ad	bronchial
3	chr3:195678000-195696200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:195679000-195691600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:195679000-195695800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:195681600-195691600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:195681600-195696200	Weak transcription	Primary B cells from cord blood	blood
8	chr3:195681800-195688600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:195681800-195688800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:195681800-195689400	Weak transcription	A549	lung
11	chr3:195681800-195691600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:195681800-195691600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:195681800-195691600	Weak transcription	Stomach Mucosa	stomach
14	chr3:195681800-195695600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:195681800-195696200	Weak transcription	HepG2	liver
16	chr3:195681800-195696400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:195681800-195696400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:195681800-195696800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:195682000-195691600	Weak transcription	HMEC	breast
20	chr3:195682600-195689400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:195682600-195689400	Weak transcription	Osteobl	bone
22	chr3:195682600-195691600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:195682600-195691600	Weak transcription	NHLF	lung
24	chr3:195682600-195693400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:195682600-195697000	Weak transcription	Fetal Lung	lung
26	chr3:195682600-195715600	Weak transcription	Psoas Muscle	Psoas
27	chr3:195682800-195688600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:195682800-195689400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:195682800-195691000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:195682800-195691600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:195682800-195696200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:195682800-195696400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:195683400-195696600	Weak transcription	HUVEC	blood vessel
34	chr3:195683600-195690400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr3:195683600-195711800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:195683800-195696400	Weak transcription	Fetal Brain Male	brain
37	chr3:195684000-195689800	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:195684000-195690200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:195684200-195711800	Strong transcription	Placenta	Placenta
40	chr3:195684600-195691600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:195685400-195690200	Strong transcription	Fetal Brain Female	brain
42	chr3:195685400-195698800	Strong transcription	Dnd41	blood
43	chr3:195685600-195690200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:195685600-195690200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:195685600-195690400	Strong transcription	Lung	lung
46	chr3:195685800-195691600	Weak transcription	Brain Anterior Caudate	brain
47	chr3:195685800-195716600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:195686000-195689400	Weak transcription	Adipose Nuclei	Adipose
49	chr3:195686000-195690800	Weak transcription	Brain Substantia Nigra	brain
50	chr3:195686000-195691400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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