Variant report

Variant	esv3349362
Chromosome Location	chr12:124575099-124580197
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF664-2	chr12:124575119-124575483	XLOC_009926
2	lnc-ZNF664-2	chr12:124575119-124576008	XLOC_009926
3	lnc-ZNF664-2	chr12:124575119-124575483	XLOC_009926
4	lnc-ZNF664-2	chr12:124575119-124575483	XLOC_009926

Variant related genes	Relation type
NUFIP2	miRNA target sites
CNOT6	miRNA target sites

Extended variants
information (count: 250 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:250 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs77205968	chr12:124575175-124575176	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
2	rs543610260	chr12:124575180-124575181	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
3	rs561682518	chr12:124575195-124575196	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
4	rs529233360	chr12:124575200-124575201	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
5	rs73411523	chr12:124575204-124575205	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs540733496	chr12:124575222-124575223	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs565926581	chr12:124575224-124575225	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs534032494	chr12:124575288-124575289	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs545143825	chr12:124575327-124575328	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs193083836	chr12:124575330-124575331	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs547874391	chr12:124575436-124575437	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs564086758	chr12:124575465-124575466	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs377117433	chr12:124575467-124575468	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs369148586	chr12:124575492-124575493	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs75113779	chr12:124575505-124575506	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs539841281	chr12:124575514-124575515	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs7971227	chr12:124575516-124575517	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs563652126	chr12:124575521-124575522	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs825481	chr12:124575558-124575559	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs825482	chr12:124575615-124575616	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs7956827	chr12:124575635-124575636	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs535205740	chr12:124575674-124575675	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs546806080	chr12:124575701-124575702	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs116142966	chr12:124575705-124575706	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs539076644	chr12:124575718-124575719	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs548661744	chr12:124575783-124575784	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs185269229	chr12:124575841-124575842	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs576405266	chr12:124575866-124575867	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs536917355	chr12:124575886-124575887	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs190614772	chr12:124575909-124575910	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs373372108	chr12:124575933-124575934	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs573784780	chr12:124575937-124575938	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs825483	chr12:124575977-124575978	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs559063936	chr12:124576061-124576062	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs112852802	chr12:124576088-124576089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs544610602	chr12:124576114-124576115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs144253804	chr12:124576135-124576136	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs825484	chr12:124576153-124576154	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs146590066	chr12:124576235-124576236	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs141348599	chr12:124576245-124576246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs577537911	chr12:124576299-124576300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs528724918	chr12:124576327-124576328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs145124160	chr12:124576365-124576366	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs825485	chr12:124576411-124576412	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs539088946	chr12:124576446-124576447	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs551015549	chr12:124576450-124576451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs569122104	chr12:124576457-124576458	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs77083678	chr12:124576504-124576505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs529196545	chr12:124576509-124576510	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs555423265	chr12:124576526-124576527	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:70)

Disease	PMID	Source
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Cancer	16751803	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Wilms tumour	21544195	CNVD
Ovarian cancer	21720365	CNVD
Colorectal cancer	16272173	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	16397240	CNVD
Breast cancer	17133270	CNVD
Breast cancer	17603634	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Schizophrenia	18923514	CNVD
Schizophrenia	22241247	CNVD
Cryptorchidism	21048976	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Neuroblastoma	18923191	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	21806811	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Prostate cancer	18632612	CNVD
Developmental delay	21457577	CNVD
dysmorphic	21457577	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Olfactory neuroblastoma	18408657	CNVD
Chordoma	18071362	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Breast cancer	22522925	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	19490664	CNVD

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124562400-124577400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:124568600-124592000	Weak transcription	Right Atrium	heart
3	chr12:124570000-124577000	Weak transcription	Pancreas	Pancrea
4	chr12:124570200-124577800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:124570800-124582200	Weak transcription	Fetal Brain Female	brain
6	chr12:124573400-124577000	Weak transcription	Fetal Kidney	kidney
7	chr12:124573400-124577200	Weak transcription	Fetal Lung	lung
8	chr12:124574200-124575200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr12:124574200-124575400	Enhancers	Fetal Stomach	stomach
10	chr12:124574600-124575200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr12:124574600-124575400	Enhancers	Gastric	stomach
12	chr12:124574600-124575800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:124574800-124575600	Enhancers	Stomach Mucosa	stomach
14	chr12:124575400-124577600	Weak transcription	Gastric	stomach
15	chr12:124575600-124578600	Weak transcription	Stomach Mucosa	stomach
16	chr12:124577000-124577400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:124577000-124578200	ZNF genes & repeats	Fetal Kidney	kidney
18	chr12:124577000-124578200	ZNF genes & repeats	Pancreas	Pancrea
19	chr12:124577200-124577400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:124577200-124578000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
21	chr12:124577200-124578000	ZNF genes & repeats	Fetal Heart	heart
22	chr12:124577200-124578200	ZNF genes & repeats	Fetal Lung	lung
23	chr12:124577400-124577600	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr12:124577400-124577600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:124577400-124578000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:124577400-124578000	ZNF genes & repeats	K562	blood
27	chr12:124577400-124578200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
28	chr12:124577600-124578200	ZNF genes & repeats	Esophagus	oesophagus
29	chr12:124577600-124578400	ZNF genes & repeats	Gastric	stomach
30	chr12:124577600-124583200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:124577800-124578000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr12:124577800-124578200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:124578000-124578200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:124578000-124578200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:124578000-124579000	Weak transcription	Spleen	Spleen
36	chr12:124578000-124579200	Weak transcription	Fetal Heart	heart
37	chr12:124578200-124578600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:124578200-124582200	Weak transcription	Fetal Kidney	kidney
39	chr12:124578200-124582200	Weak transcription	Fetal Lung	lung
40	chr12:124578200-124582800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:124578400-124578600	Weak transcription	Pancreas	Pancrea
42	chr12:124578400-124578800	Weak transcription	Gastric	stomach
43	chr12:124578400-124579000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr12:124578400-124579600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr12:124578400-124581400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:124578600-124580000	Enhancers	Stomach Mucosa	stomach
47	chr12:124578800-124579600	Enhancers	Gastric	stomach
48	chr12:124579000-124579400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr12:124579000-124579600	Enhancers	Fetal Muscle Leg	muscle
50	chr12:124579000-124579800	Enhancers	Spleen	Spleen

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