Variant report

Variant	nsv557748
Chromosome Location	chr12:21815529-21816831
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:21816693-21816731	GM10248	blood:	n/a	n/a
2	MAX	chr12:21815247-21815871	A549	lung:	n/a	n/a
3	POLR2A	chr12:21815658-21815669	A549	lung:	n/a	n/a
4	POLR2A	chr12:21815126-21815604	A549	lung:	n/a	n/a
5	POLR2A	chr12:21815143-21815606	A549	lung:	n/a	n/a
6	POLR2A	chr12:21815642-21815657	A549	lung:	n/a	n/a
7	RAD21	chr12:21815551-21815727	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:21815512-21815562	HCPEpiC	choroid plexus:	n/a
2	chr12:21815512-21815562	ProgFib	skin:	n/a
3	chr12:21815512-21815562	Hela-S3	cervix:	n/a
4	chr12:21815512-21815562	PrEC	prostate:	n/a
5	chr12:21815512-21815562	HNPCEpiC	eye:	n/a
6	chr12:21815512-21815562	Caco-2	colon:	n/a
7	chr12:21815512-21815562	SK-N-SH_RA	brain:	n/a
8	chr12:21815512-21815562	HCM	heart:	n/a
9	chr12:21815512-21815562	NHDF-neo	bronchial:	n/a
10	chr12:21815512-21815562	BE2_C	brain:	n/a
11	chr12:21815512-21815562	IMR90	lung:	fetal
12	chr12:21815512-21815562	GM19239	blood:	n/a
13	chr12:21815512-21815562	Hepatocyte	liver:	n/a
14	chr12:21815512-21815562	HUVEC	blood vessel:	n/a
15	chr12:21815512-21815562	NHBE	bronchial:	n/a
16	chr12:21815512-21815562	AG10803	skin:	n/a
17	chr12:21815512-21815562	GM12892	blood:	n/a
18	chr12:21815512-21815562	ECC-1	luminal epithelium:	n/a
19	chr12:21815512-21815562	AG09319	gingival:	n/a
20	chr12:21815512-21815562	HEK293	kidney:	embryo
21	chr12:21815512-21815562	SK-N-SH	brain:	n/a
22	chr12:21815512-21815562	RPTEC	kidney:	n/a
23	chr12:21815512-21815562	HIPEpiC	eye:	n/a
24	chr12:21815512-21815562	BJ	skin:	n/a
25	chr12:21815512-21815562	GM12891	blood:	n/a
26	chr12:21815512-21815562	AG04450	lung:	fetal
27	chr12:21815512-21815562	PANC-1	pancreas:	n/a
28	chr12:21815512-21815562	GM12878	blood:	n/a
29	chr12:21815512-21815562	SK-N-MC	brain:	n/a
30	chr12:21815512-21815562	U87	brain:	n/a
31	chr12:21815512-21815562	HepG2	liver:	n/a
32	chr12:21815512-21815562	HMEC	breast:	n/a
33	chr12:21815512-21815562	HCT-116	colon:	n/a
34	chr12:21815512-21815562	HCF	heart:	n/a
35	chr12:21815512-21815562	AoSMC	blood vessel:	n/a
36	chr12:21815512-21815562	ovcar-3	ovarian:	n/a
37	chr12:21815512-21815562	AG04449	skin:	fetal
38	chr12:21815512-21815562	LNCaP	prostate:	n/a
39	chr12:21815512-21815562	A549	lung:	n/a
40	chr12:21815512-21815562	SAEC	small airway:	n/a
41	chr12:21815512-21815562	NH-A	brain:	n/a
42	chr12:21815512-21815562	AG09309	skin:	n/a
43	chr12:21815512-21815562	HAEpiC	amniotic membrane:	n/a
44	chr12:21815512-21815562	HRE	kidney:	n/a
45	chr12:21815512-21815562	T-47D	breast:	n/a
46	chr12:21815512-21815562	HPAEpiC	pulmonary alveolar:	n/a
47	chr12:21815512-21815562	HL-60	blood:	n/a
48	chr12:21815512-21815562	CMK	blood:	n/a
49	chr12:21815512-21815562	Jurkat	blood:	n/a
50	chr12:21815512-21815562	MCF10A-Er-Src	breast:	n/a

No data

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf39-1	chr12:21815247-21815705	ENSG00000256615.1

No data

Variant related genes	Relation type
LDHB	TF binding region
LDHB	CpG island

Extended variants
information (count: 119 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:119 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs59805820	chr12:21815537-21815538	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs184665633	chr12:21815546-21815547	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs567317103	chr12:21815547-21815548	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs559298723	chr12:21815561-21815562	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs536571451	chr12:21815562-21815563	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs74184609	chr12:21815564-21815565	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	mRNA abundance
7	rs570459497	chr12:21815565-21815566	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs112041439	chr12:21815577-21815578	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs73077300	chr12:21815580-21815581	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs187443974	chr12:21815602-21815603	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs371583481	chr12:21815606-21815607	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs79662965	chr12:21815607-21815608	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs191934168	chr12:21815609-21815610	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs191383545	chr12:21815610-21815611	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs78929102	chr12:21815612-21815613	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	mRNA abundance
16	rs555225048	chr12:21815624-21815625	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs543476910	chr12:21815643-21815644	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs563928579	chr12:21815648-21815649	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs76654229	chr12:21815650-21815651	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	mRNA abundance
20	rs376407548	chr12:21815662-21815663	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs73262354	chr12:21815663-21815664	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs80042173	chr12:21815665-21815666	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	mRNA abundance
23	rs146857244	chr12:21815669-21815670	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs200405782	chr12:21815671-21815672	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs551397853	chr12:21815672-21815673	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs564831179	chr12:21815677-21815678	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs192760359	chr12:21815680-21815681	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs577273892	chr12:21815705-21815706	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs66978947	chr12:21815725-21815726	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs114895869	chr12:21815735-21815736	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs184168131	chr12:21815764-21815765	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs546765042	chr12:21815766-21815767	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs562889936	chr12:21815772-21815773	Weak transcription Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs12826014	chr12:21815800-21815801	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs146706252	chr12:21815801-21815802	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs557745170	chr12:21815810-21815811	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs12824936	chr12:21815820-21815821	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs114407226	chr12:21815835-21815836	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs557206795	chr12:21815839-21815840	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs72276276	chr12:21815875-21815876	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs574068426	chr12:21815876-21815877	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs75832204	chr12:21815881-21815882	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs12824788	chr12:21815898-21815899	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
44	rs139292160	chr12:21815922-21815923	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs545685086	chr12:21815941-21815942	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs564897696	chr12:21815955-21815956	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs12825320	chr12:21815979-21815980	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs372675065	chr12:21815988-21815989	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs190784007	chr12:21815996-21815997	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs71452236	chr12:21816004-21816005	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Malignant germ cell tumour	17285132	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Myxofibrosarcoma	16751306	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Acute myeloid leukemia	16864856	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
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
Testicular germ cell tumor	18059402	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	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17133270	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	16397240	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21364760	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	21509527	CNVD
Autism	22102821	CNVD
Follicular lymphoma	18703704	CNVD
Lung cancer	18438408	CNVD
Lung cancer	21911935	CNVD
Breast cancer	22048815	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16272173	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Heart disease	21282601	CNVD
Ovarian cancer	20844748	CNVD
Lung cancer	17925434	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Gastric cancer	24379144	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Gastric cancer	19545448	CNVD
Lung cancer	20031968	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung adenocarcinoma	19826477	CNVD
Lung cancer	19525976	CNVD
Lung cancer	19826477	CNVD
Non-small cell lung cancer	19451690	CNVD
Non-small cell lung cancer	17504988	CNVD
Bipolar disorder	19114987	CNVD
Lung cancer	19671679	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21810800-21816400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:21815400-21815600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr12:21815400-21815800	Active TSS	Muscle Satellite Cultured Cells	--
4	chr12:21815400-21815800	Active TSS	Fetal Muscle Trunk	muscle
5	chr12:21815400-21816000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
6	chr12:21815400-21816200	Active TSS	A549	lung
7	chr12:21815600-21815800	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr12:21815800-21816000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
9	chr12:21816200-21818800	Weak transcription	A549	lung
10	chr12:21816400-21817000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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