Variant report

Variant	esv1831762
Chromosome Location	chr3:84940927-84954574
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr3:84954233-84954576	HepG2	liver:	n/a	n/a
2	CTCF	chr3:84950160-84950310	GM12867	blood:	n/a	n/a
3	CTCF	chr3:84950240-84950390	HUVEC	blood vessel:	n/a	n/a
4	E2F4	chr3:84942003-84942163	MCF10A-Er-Src	breast:	n/a	n/a
5	FOXA1	chr3:84943756-84944012	T-47D	breast:	n/a	n/a
6	FOXA1	chr3:84943708-84944084	T-47D	breast:	n/a	n/a
7	FOXA1	chr3:84942280-84942716	T-47D	breast:	n/a	n/a
8	FOXA1	chr3:84942336-84942612	T-47D	breast:	n/a	n/a
9	GATA3	chr3:84942231-84942744	T-47D	breast:	n/a	chr3:84942340-84942350
10	GATA3	chr3:84943744-84944001	SH-SY5Y	brain:	n/a	n/a
11	GATA3	chr3:84945858-84946175	T-47D	breast:	n/a	n/a
12	GATA3	chr3:84943614-84944114	T-47D	breast:	n/a	n/a
13	GATA3	chr3:84941026-84941169	SH-SY5Y	brain:	n/a	chr3:84941145-84941155 chr3:84941146-84941153 chr3:84941146-84941153 chr3:84941146-84941153
14	GATA3	chr3:84945849-84946149	T-47D	breast:	n/a	n/a
15	GATA3	chr3:84942290-84942748	T-47D	breast:	n/a	chr3:84942340-84942350
16	GATA3	chr3:84943690-84944127	T-47D	breast:	n/a	n/a
17	MAFK	chr3:84952074-84952262	HepG2	liver:	n/a	chr3:84952232-84952247
18	MAFK	chr3:84951991-84952306	HepG2	liver:	n/a	chr3:84952232-84952247
19	MYC	chr3:84954337-84954511	MCF-7	breast:	n/a	n/a
20	POLR2A	chr3:84947069-84947239	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr3:84954156-84954217	A549	lung:	n/a	n/a
22	POLR2A	chr3:84954075-84954096	MCF-7	breast:	n/a	n/a
23	POLR2A	chr3:84954049-84954648	MCF-7	breast:	n/a	n/a
24	POLR2A	chr3:84954107-84954160	MCF-7	breast:	n/a	n/a
25	POLR2A	chr3:84950848-84950900	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:84954118-84954141	A549	lung:	n/a	n/a
27	POLR2A	chr3:84954264-84954422	A549	lung:	n/a	n/a
28	POLR2A	chr3:84954177-84954297	MCF-7	breast:	n/a	n/a
29	POLR2A	chr3:84954260-84954262	Gliobla	brain:	n/a	n/a
30	POLR2A	chr3:84954378-84954393	MCF-7	breast:	n/a	n/a
31	SIN3A	chr3:84954186-84954285	H1-hESC	embryonic stem cell:	n/a	n/a
32	STAT3	chr3:84943493-84943677	MCF10A-Er-Src	breast:	n/a	n/a
33	STAT3	chr3:84943137-84943155	MCF10A-Er-Src	breast:	n/a	n/a
34	USF1	chr3:84953442-84953668	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF1	chr3:84953464-84953654	H1-hESC	embryonic stem cell:	n/a	n/a
36	USF1	chr3:84953448-84953670	SK-N-SH_RA	brain:	n/a	n/a
37	ZNF143	chr3:84954222-84954251	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CADM2-1	chr3:84942393-84942530	XLOC_002723
2	lnc-CADM2-1	chr3:84942083-84942116	XLOC_002723
3	lnc-CADM2-1	chr3:84942392-84942530	NONHSAT090654
4	lnc-CADM2-1	chr3:84942082-84942116	NONHSAT090654

Variant related genes	Relation type
ENSG00000266025	TF binding region
THAP6	miRNA target sites
YES1	miRNA target sites

Extended variants
information (count: 64 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:64 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs142798316	chr3:84942091-84942092	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs571252733	chr3:84942106-84942107	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs114957109	chr3:84942107-84942108	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs189518973	chr3:84950216-84950217	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs535694120	chr3:84950222-84950223	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs554243447	chr3:84950247-84950248	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs114601647	chr3:84950248-84950249	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs554573376	chr3:84950249-84950250	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs182048451	chr3:84950254-84950255	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs574617720	chr3:84950263-84950264	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs576795436	chr3:84950269-84950270	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs540307336	chr3:84950285-84950286	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs544157171	chr3:84950352-84950353	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs143807647	chr3:84950360-84950361	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs553647776	chr3:84950369-84950370	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs111228823	chr3:84950374-84950375	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs574675132	chr3:84950375-84950376	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs113087543	chr3:84950885-84950886	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs182236895	chr3:84952005-84952006	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs145085853	chr3:84952106-84952107	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs539984142	chr3:84952125-84952126	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs139991363	chr3:84952143-84952144	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs547363649	chr3:84952196-84952197	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs565922181	chr3:84952244-84952245	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs539364073	chr3:84952285-84952286	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs188323705	chr3:84952290-84952291	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs57155100	chr3:84952298-84952299	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs115776078	chr3:84953446-84953447	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs575961143	chr3:84953563-84953564	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs1691487	chr3:84953580-84953581	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs560407438	chr3:84953583-84953584	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs555175259	chr3:84953587-84953588	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs36107387	chr3:84953641-84953642	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs1694958	chr3:84953642-84953643	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs559223477	chr3:84953643-84953644	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs114557692	chr3:84953655-84953656	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs1694957	chr3:84953865-84953866	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs184868936	chr3:84953866-84953867	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs548886567	chr3:84953922-84953923	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs1691485	chr3:84953926-84953927	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs548492303	chr3:84953951-84953952	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs547058332	chr3:84953952-84953953	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs1691484	chr3:84953992-84953993	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs111593496	chr3:84953997-84953998	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs539124222	chr3:84954003-84954004	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs73135623	chr3:84954030-84954031	Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs569297073	chr3:84954061-84954062	Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs536926277	chr3:84954074-84954075	Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs34496036	chr3:84954105-84954106	Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs555338896	chr3:84954167-84954168	Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:79)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Melanoma	18172304	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Wilms tumour	21544195	CNVD
Colorectal cancer	16272173	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Soft tissue tumor	16732325	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Mental retardation	17124404	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Schizophrenia	23813976	CNVD
Lung squamous cell carcinoma	22363434	CNVD
Autism	22102821	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:84953800-84955600	Enhancers	Fetal Muscle Leg	muscle
2	chr3:84954000-84954200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:84954000-84954200	Enhancers	Psoas Muscle	Psoas
4	chr3:84954000-84954200	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr3:84954000-84954200	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:84954000-84955600	Enhancers	Fetal Muscle Trunk	muscle
7	chr3:84954200-84954600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:84954200-84954600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:84954200-84954600	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:84954200-84954600	Flanking Active TSS	Psoas Muscle	Psoas
11	chr3:84954200-84954600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:84954200-84955400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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