Variant report

Variant	esv3519227
Chromosome Location	chr2:133670682-133675580
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr2:133671660-133671837	MCF10A-Er-Src	breast:	n/a	n/a
2	EBF1	chr2:133673346-133673757	GM12878	blood:	n/a	chr2:133673624-133673637 chr2:133673624-133673635 chr2:133673626-133673636 chr2:133673626-133673635
3	POLR2A	chr2:133673706-133674218	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr2:133673732-133674203	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr2:133671701-133671775	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:133672682-133672732	AG04450	lung:	fetal
2	chr2:133672682-133672732	NHDF-neo	bronchial:	n/a
3	chr2:133672682-133672732	ovcar-3	ovarian:	n/a
4	chr2:133672682-133672732	BE2_C	brain:	n/a
5	chr2:133672682-133672732	NB4	blood:	n/a
6	chr2:133672682-133672732	Caco-2	colon:	n/a
7	chr2:133672682-133672732	HRPEpiC	eye:	n/a
8	chr2:133672682-133672732	HPAEpiC	pulmonary alveolar:	n/a
9	chr2:133672682-133672732	Hepatocyte	liver:	n/a
10	chr2:133672682-133672732	LNCaP	prostate:	n/a
11	chr2:133672682-133672732	K562	blood:	n/a
12	chr2:133672682-133672732	HCPEpiC	choroid plexus:	n/a
13	chr2:133672682-133672732	AG10803	skin:	n/a
14	chr2:133672682-133672732	HCF	heart:	n/a
15	chr2:133672682-133672732	NH-A	brain:	n/a
16	chr2:133672682-133672732	NT2-D1	testis:	n/a
17	chr2:133672682-133672732	GM12891	blood:	n/a
18	chr2:133672682-133672732	IMR90	lung:	fetal
19	chr2:133672682-133672732	SKMC	muscle:	n/a
20	chr2:133672682-133672732	T-47D	breast:	n/a
21	chr2:133672682-133672732	PFSK-1	brain:	n/a
22	chr2:133672682-133672732	HRCEpiC	kidney:	n/a
23	chr2:133672682-133672732	HAEpiC	amniotic membrane:	n/a
24	chr2:133672682-133672732	HUVEC	blood vessel:	n/a
25	chr2:133672682-133672732	HMEC	breast:	n/a
26	chr2:133672682-133672732	HNPCEpiC	eye:	n/a
27	chr2:133672682-133672732	AoSMC	blood vessel:	n/a
28	chr2:133672682-133672732	RPTEC	kidney:	n/a
29	chr2:133672682-133672732	SK-N-SH	brain:	n/a
30	chr2:133672682-133672732	SK-N-MC	brain:	n/a
31	chr2:133672682-133672732	GM12878	blood:	n/a
32	chr2:133672682-133672732	H1-hESC	embryonic stem cell:	embryo
33	chr2:133672682-133672732	SAEC	small airway:	n/a
34	chr2:133672682-133672732	HL-60	blood:	n/a
35	chr2:133672682-133672732	HIPEpiC	eye:	n/a
36	chr2:133672682-133672732	AG09319	gingival:	n/a
37	chr2:133672682-133672732	U87	brain:	n/a
38	chr2:133672682-133672732	Jurkat	blood:	n/a
39	chr2:133672682-133672732	HRE	kidney:	n/a
40	chr2:133672682-133672732	GM06990	blood:	n/a
41	chr2:133672682-133672732	A549	lung:	n/a
42	chr2:133672682-133672732	GM12892	blood:	n/a
43	chr2:133672682-133672732	HCM	heart:	n/a
44	chr2:133672682-133672732	HEEpiC	esophagus:	n/a
45	chr2:133672682-133672732	GM19239	blood:	n/a
46	chr2:133672682-133672732	HepG2	liver:	n/a
47	chr2:133672682-133672732	ProgFib	skin:	n/a
48	chr2:133672682-133672732	CMK	blood:	n/a
49	chr2:133672682-133672732	SK-N-SH_RA	brain:	n/a
50	chr2:133672682-133672732	HCT-116	colon:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR39-3	chr2:133673130-133673224	ENSG00000233729.1

No data

Variant related genes	Relation type
ENSG00000228721	TF binding region
ENSG00000233729	TF binding region
ENSG00000228721	CpG island
ENSG00000233729	CpG island

Extended variants
information (count: 148 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:148 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs539335902	chr2:133670692-133670693	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs558923316	chr2:133670710-133670711	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs1447541	chr2:133670711-133670712	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs540095225	chr2:133670763-133670764	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs535384427	chr2:133670818-133670819	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs541525624	chr2:133670891-133670892	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs77012455	chr2:133670943-133670944	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs1447545	chr2:133671009-133671010	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs542047205	chr2:133671081-133671082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs191169760	chr2:133671086-133671087	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs531126800	chr2:133671089-133671090	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs552568074	chr2:133671142-133671143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs180930468	chr2:133671158-133671159	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs75983540	chr2:133671197-133671198	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs545747862	chr2:133671210-133671211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs79489665	chr2:133671268-133671269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs10175655	chr2:133671270-133671271	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs185356415	chr2:133671382-133671383	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs550825428	chr2:133671444-133671445	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs147257417	chr2:133671450-133671451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs190117777	chr2:133671489-133671490	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs557729847	chr2:133671525-133671526	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs566752061	chr2:133671591-133671592	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs376234557	chr2:133671635-133671636	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs552930859	chr2:133671669-133671670	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
26	rs182750788	chr2:133671733-133671734	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
27	rs541887634	chr2:133671781-133671782	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
28	rs531883571	chr2:133671805-133671806	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
29	rs557156393	chr2:133671859-133671860	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs575702955	chr2:133671860-133671861	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs546484050	chr2:133671861-133671862	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs557751586	chr2:133671928-133671929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs186034220	chr2:133671930-133671931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs140689301	chr2:133671952-133671953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs539873349	chr2:133671958-133671959	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs572967440	chr2:133671987-133671988	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs537940489	chr2:133672008-133672009	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs561648860	chr2:133672073-133672074	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs374350497	chr2:133672109-133672110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs548398686	chr2:133672151-133672152	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs540363844	chr2:133672186-133672187	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs555975179	chr2:133672228-133672229	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs550664943	chr2:133672241-133672242	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs58379322	chr2:133672351-133672352	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs562120610	chr2:133672357-133672358	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs191962198	chr2:133672358-133672359	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs55848608	chr2:133672374-133672375	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs566683672	chr2:133672394-133672395	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs534079201	chr2:133672404-133672405	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs552965705	chr2:133672443-133672444	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
Breast cancer	16272173	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
lymphocytic leukemia	21291569	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Colorectal cancer	16272173	CNVD
myoclonus epilepsy	18472482	CNVD
Benign familial neonatal-infantile seizures	18472482	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	18632612	CNVD
Developmental delay	21147756	CNVD
Mental retardation	17621639	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Breast cancer	21509527	CNVD
Mental retardation	17124404	CNVD
Colorectal cancer	20459617	CNVD
Neuroticism	17667963	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	22522925	CNVD
Oral cancer	21386901	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133667200-133681600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:133667600-133673000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:133668800-133676400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:133669800-133672600	Weak transcription	Adipose Nuclei	Adipose
5	chr2:133669800-133672800	Weak transcription	Fetal Lung	lung
6	chr2:133669800-133672800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:133670200-133672800	Weak transcription	Fetal Muscle Leg	muscle
8	chr2:133670400-133672600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:133670400-133673400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:133672200-133673600	Enhancers	Fetal Heart	heart
11	chr2:133672600-133673000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:133672600-133674200	Enhancers	Adipose Nuclei	Adipose
13	chr2:133672800-133673000	Enhancers	Lung	lung
14	chr2:133672800-133673200	Enhancers	Fetal Muscle Trunk	muscle
15	chr2:133672800-133673400	Enhancers	Fetal Muscle Leg	muscle
16	chr2:133672800-133673400	Enhancers	Right Atrium	heart
17	chr2:133672800-133674000	Enhancers	Fetal Lung	lung
18	chr2:133672800-133674000	Enhancers	Right Ventricle	heart
19	chr2:133672800-133674400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:133673000-133674200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:133673000-133681000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:133673200-133674000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:133673400-133674000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:133673600-133688800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:133673800-133674000	Enhancers	Lung	lung
26	chr2:133674000-133676400	Weak transcription	Fetal Lung	lung

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