Variant report

Variant	esv3416921
Chromosome Location	chr3:97859875-97902358
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	BCL11A	chr3:97895161-97895345	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:97873705-97874032	HepG2	liver:	n/a	chr3:97873850-97873861
3	CTCF	chr3:97884218-97884248	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr3:97887450-97887549	Medullo	brain:	n/a	n/a
5	CTCF	chr3:97884135-97884303	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr3:97884207-97884295	HepG2	liver:	n/a	n/a
7	CTCF	chr3:97887528-97887558	GM10266	blood:	n/a	n/a
8	CTCF	chr3:97868194-97868279	GM10266	blood:	n/a	n/a
9	CTCF	chr3:97868196-97868256	GM13977	blood:	n/a	n/a
10	CTCF	chr3:97884180-97884330	HepG2	liver:	n/a	n/a
11	CTCF	chr3:97882688-97882729	GM10248	blood:	n/a	n/a
12	CTCF	chr3:97884129-97884304	HepG2	liver:	n/a	n/a
13	CTCF	chr3:97865477-97865502	Spleen_OC	spleen:	n/a	n/a
14	CTCF	chr3:97868287-97868395	Lung_OC	lung:	n/a	n/a
15	CTCF	chr3:97869056-97869117	GM10248	blood:	n/a	n/a
16	E2F4	chr3:97892081-97892199	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr3:97870123-97870337	MCF10A-Er-Src	breast:	n/a	chr3:97870231-97870240 chr3:97870231-97870241 chr3:97870233-97870240 chr3:97870232-97870241
18	FOS	chr3:97870109-97870426	MCF10A-Er-Src	breast:	n/a	chr3:97870114-97870123 chr3:97870231-97870240 chr3:97870231-97870241 chr3:97870233-97870240 chr3:97870232-97870241
19	FOS	chr3:97870223-97870394	MCF10A-Er-Src	breast:	n/a	chr3:97870231-97870240 chr3:97870231-97870241 chr3:97870233-97870240 chr3:97870232-97870241
20	FOS	chr3:97870114-97870399	MCF10A-Er-Src	breast:	n/a	chr3:97870114-97870123 chr3:97870231-97870240 chr3:97870231-97870241 chr3:97870233-97870240 chr3:97870232-97870241
21	FOXA1	chr3:97883878-97884461	HepG2	liver:	n/a	n/a
22	FOXA1	chr3:97884094-97884386	HepG2	liver:	n/a	n/a
23	FOXA1	chr3:97884116-97884437	HepG2	liver:	n/a	n/a
24	FOXA1	chr3:97885429-97885735	T-47D	breast:	n/a	n/a
25	FOXA2	chr3:97893171-97893709	A549	lung:	n/a	n/a
26	FOXA2	chr3:97884127-97884371	HepG2	liver:	n/a	n/a
27	JUND	chr3:97884273-97884415	HepG2	liver:	n/a	n/a
28	JUND	chr3:97870047-97870402	HepG2	liver:	n/a	chr3:97870114-97870123 chr3:97870231-97870240 chr3:97870231-97870241 chr3:97870233-97870240 chr3:97870230-97870241 chr3:97870232-97870241
29	MAFK	chr3:97864781-97864990	HepG2	liver:	n/a	n/a
30	MAFK	chr3:97874784-97875019	HepG2	liver:	n/a	chr3:97874923-97874939 chr3:97874928-97874939 chr3:97874928-97874939 chr3:97874927-97874938 chr3:97874927-97874938 chr3:97874926-97874940
31	MAX	chr3:97891592-97891756	HepG2	liver:	n/a	n/a
32	MXI1	chr3:97891052-97891233	GM12878	blood:	n/a	n/a
33	MYC	chr3:97899439-97899676	MCF10A-Er-Src	breast:	n/a	n/a
34	NFE2	chr3:97899510-97899549	GM12878	blood:	n/a	n/a
35	NFYA	chr3:97873667-97873855	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:97900066-97900090	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr3:97881950-97882071	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr3:97887487-97887525	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr3:97873717-97873719	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr3:97863328-97863432	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr3:97862532-97862662	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:97881652-97881656	A549	lung:	n/a	n/a
43	RAD21	chr3:97884113-97884360	HepG2	liver:	n/a	n/a
44	RAD21	chr3:97884057-97884404	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr3:97884112-97884312	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr3:97884108-97884333	H1-hESC	embryonic stem cell:	n/a	n/a
47	RXRA	chr3:97884021-97884408	HepG2	liver:	n/a	n/a
48	SP1	chr3:97883988-97884430	HepG2	liver:	n/a	n/a
49	SPI1	chr3:97899164-97899487	GM12878	blood:	n/a	n/a
50	SPI1	chr3:97876149-97876511	HL-60	blood:	n/a	chr3:97876278-97876291 chr3:97876277-97876290 chr3:97876354-97876367 chr3:97876280-97876287

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:97887864-97887914	Hepatocyte	liver:	n/a
2	chr3:97887864-97887914	Hepatocyte	liver:	n/a
3	chr3:97887864-97887914	AG10803	skin:	n/a
4	chr3:97868656-97868706	HRE	kidney:	n/a
5	chr3:97868656-97868706	AG09309	skin:	n/a
6	chr3:97887864-97887914	Jurkat	blood:	n/a
7	chr3:97867758-97867808	GM12892	blood:	n/a
8	chr3:97887864-97887914	SK-N-MC	brain:	n/a
9	chr3:97887864-97887914	ovcar-3	ovarian:	n/a
10	chr3:97886467-97886517	NT2-D1	testis:	n/a
11	chr3:97886603-97886653	HCF	heart:	n/a
12	chr3:97867758-97867808	Hela-S3	cervix:	n/a
13	chr3:97868656-97868706	HCF	heart:	n/a
14	chr3:97867758-97867808	PANC-1	pancreas:	n/a
15	chr3:97887864-97887914	NT2-D1	testis:	n/a
16	chr3:97887864-97887914	HepG2	liver:	n/a
17	chr3:97886467-97886517	HPAEpiC	pulmonary alveolar:	n/a
18	chr3:97886603-97886653	MCF-7	breast:	n/a
19	chr3:97867758-97867808	Caco-2	colon:	n/a
20	chr3:97868656-97868706	U87	brain:	n/a
21	chr3:97868656-97868706	HL-60	blood:	n/a
22	chr3:97887864-97887914	K562	blood:	n/a
23	chr3:97867758-97867808	NHBE	bronchial:	n/a
24	chr3:97868656-97868706	Hela-S3	cervix:	n/a
25	chr3:97887864-97887914	Caco-2	colon:	n/a
26	chr3:97886467-97886517	HRPEpiC	eye:	n/a
27	chr3:97886603-97886653	A549	lung:	n/a
28	chr3:97868656-97868706	IMR90	lung:	fetal
29	chr3:97886467-97886517	Hepatocyte	liver:	n/a
30	chr3:97886467-97886517	AG04450	lung:	fetal
31	chr3:97887864-97887914	A549	lung:	n/a
32	chr3:97867758-97867808	AG04449	skin:	fetal
33	chr3:97886467-97886517	GM12891	blood:	n/a
34	chr3:97868656-97868706	T-47D	breast:	n/a
35	chr3:97867758-97867808	IMR90	lung:	fetal
36	chr3:97867758-97867808	HCT-116	colon:	n/a
37	chr3:97887864-97887914	ECC-1	luminal epithelium:	n/a
38	chr3:97886467-97886517	H1-hESC	embryonic stem cell:	embryo
39	chr3:97886603-97886653	HAEpiC	amniotic membrane:	n/a
40	chr3:97867758-97867808	HL-60	blood:	n/a
41	chr3:97886603-97886653	AoSMC	blood vessel:	n/a
42	chr3:97867758-97867808	GM12878	blood:	n/a
43	chr3:97868656-97868706	HEEpiC	esophagus:	n/a
44	chr3:97867758-97867808	AG09319	gingival:	n/a
45	chr3:97868656-97868706	AoSMC	blood vessel:	n/a
46	chr3:97887864-97887914	NB4	blood:	n/a
47	chr3:97867758-97867808	HRCEpiC	kidney:	n/a
48	chr3:97868656-97868706	GM19239	blood:	n/a
49	chr3:97887864-97887914	HAEpiC	amniotic membrane:	n/a
50	chr3:97868656-97868706	SK-N-MC	brain:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MINA-1	chr3:97866885-97866978	ENSG00000249225.1

Variant related genes	Relation type
OR5H14	TF binding region
OR5H15	TF binding region
ENSG00000249225	TF binding region
OR5H14	CpG island
OR5H15	CpG island
ENSG00000249225	CpG island

Extended variants
information (count: 727 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:727 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs537181985	chr3:97859888-97859889	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs72927923	chr3:97859890-97859891	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs567501020	chr3:97859892-97859893	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs144031511	chr3:97859895-97859896	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs72927924	chr3:97859905-97859906	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs72927927	chr3:97859931-97859932	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs189423409	chr3:97859939-97859940	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs75614871	chr3:97859948-97859949	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs558615774	chr3:97860014-97860015	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs575398023	chr3:97860015-97860016	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs544336588	chr3:97860022-97860023	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs374837958	chr3:97860074-97860075	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs561218680	chr3:97860079-97860080	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs542914648	chr3:97860080-97860081	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs573166765	chr3:97860119-97860120	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs112336479	chr3:97860129-97860130	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs113092670	chr3:97860145-97860146	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs146412620	chr3:97860175-97860176	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs181059413	chr3:97860200-97860201	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs112697817	chr3:97860205-97860206	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs530909356	chr3:97860239-97860240	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs111664752	chr3:97860265-97860266	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs372850963	chr3:97860283-97860284	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs72325543	chr3:97860284-97860285	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs200287020	chr3:97860293-97860294	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs60927749	chr3:97860299-97860300	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs145876517	chr3:97860313-97860314	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs536461787	chr3:97860316-97860317	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs369342423	chr3:97860332-97860333	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs372559742	chr3:97860333-97860334	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs66558448	chr3:97860334-97860335	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs386397361	chr3:97860339-97860340	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs60057798	chr3:97860341-97860342	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs546550968	chr3:97860351-97860352	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs13074270	chr3:97860355-97860356	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs13093826	chr3:97860359-97860360	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs185118435	chr3:97860375-97860376	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs538971867	chr3:97860396-97860397	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs181069452	chr3:97860410-97860411	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs138501980	chr3:97860420-97860421	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs568922061	chr3:97860474-97860475	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs149189361	chr3:97860486-97860487	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs554662829	chr3:97860493-97860494	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs565211798	chr3:97860523-97860524	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs574120451	chr3:97860578-97860579	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs138652055	chr3:97860648-97860649	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs540061452	chr3:97860649-97860650	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs544129734	chr3:97860654-97860655	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs543182709	chr3:97860655-97860656	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs143695999	chr3:97860656-97860657	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	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
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22522925	CNVD
Chordoma	21215367	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:97858200-97860000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr3:97858200-97866400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:97859800-97860800	Enhancers	Fetal Brain Male	brain
4	chr3:97860000-97860200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:97870000-97870600	Enhancers	Fetal Heart	heart
6	chr3:97889000-97890800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:97899200-97899400	Active TSS	Monocytes-CD14+_RO01746	blood
8	chr3:97899400-97899800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr3:97899400-97900000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr3:97899400-97900800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:97900000-97900200	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr3:97900400-97902000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:97900400-97902400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr3:97901000-97901800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr3:97901000-97902200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:97901400-97902000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:97901400-97902000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:97901400-97902200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:97902000-97907000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:97902200-97906400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:97902200-97907200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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