Variant report

Variant	nsv591063
Chromosome Location	chr3:97924688-97958280
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	BATF	chr3:97952380-97952574	GM12878	blood:	n/a	n/a
2	BCL11A	chr3:97952351-97952515	GM12878	blood:	n/a	n/a
3	BCL11A	chr3:97951400-97951563	GM12878	blood:	n/a	n/a
4	BHLHE40	chr3:97951405-97952685	GM12878	blood:	n/a	n/a
5	BHLHE40	chr3:97943474-97943485	GM12878	blood:	n/a	n/a
6	BRCA1	chr3:97939937-97940001	GM12878	blood:	n/a	n/a
7	CHD1	chr3:97952484-97952829	GM12878	blood:	n/a	n/a
8	CHD1	chr3:97942962-97942975	GM12878	blood:	n/a	n/a
9	CHD2	chr3:97952077-97952654	GM12878	blood:	n/a	n/a
10	CTCF	chr3:97952320-97952470	GM12872	blood:	n/a	n/a
11	CTCF	chr3:97952340-97952490	GM06990	blood:	n/a	n/a
12	CTCF	chr3:97952360-97952510	GM12873	blood:	n/a	n/a
13	CTCF	chr3:97952340-97952490	GM12873	blood:	n/a	n/a
14	CTCF	chr3:97926264-97926295	LNCaP	prostate:	n/a	n/a
15	CTCF	chr3:97952400-97952550	GM12868	blood:	n/a	n/a
16	CTCF	chr3:97957348-97957372	GM13977	blood:	n/a	n/a
17	CTCF	chr3:97952380-97952530	GM12878	blood:	n/a	n/a
18	CUX1	chr3:97954941-97955041	GM12878	blood:	n/a	n/a
19	CUX1	chr3:97951097-97951764	GM12878	blood:	n/a	n/a
20	CUX1	chr3:97952186-97952580	GM12878	blood:	n/a	n/a
21	CUX1	chr3:97950242-97950304	GM12878	blood:	n/a	n/a
22	E2F4	chr3:97956249-97956436	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F4	chr3:97925082-97925346	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F6	chr3:97945258-97945608	H1-hESC	embryonic stem cell:	n/a	n/a
25	EBF1	chr3:97942889-97943689	GM12878	blood:	n/a	n/a
26	EBF1	chr3:97952295-97952631	GM12878	blood:	n/a	n/a
27	EBF1	chr3:97953388-97953441	GM12878	blood:	n/a	n/a
28	EBF1	chr3:97952104-97952725	GM12878	blood:	n/a	n/a
29	EBF1	chr3:97952207-97952623	GM12878	blood:	n/a	n/a
30	EBF1	chr3:97950253-97951851	GM12878	blood:	n/a	n/a
31	EBF1	chr3:97954436-97955224	GM12878	blood:	n/a	chr3:97954988-97954999 chr3:97954989-97954999 chr3:97954988-97955001 chr3:97954990-97954999
32	EBF1	chr3:97955751-97955777	GM12878	blood:	n/a	n/a
33	ELK1	chr3:97950909-97950973	GM12878	blood:	n/a	n/a
34	EP300	chr3:97950308-97950601	GM12878	blood:	n/a	chr3:97950574-97950588
35	EP300	chr3:97952127-97952625	GM12878	blood:	n/a	n/a
36	EP300	chr3:97942493-97942522	GM12878	blood:	n/a	n/a
37	EP300	chr3:97942865-97943065	GM12878	blood:	n/a	chr3:97942875-97942884 chr3:97942874-97942883
38	EP300	chr3:97943284-97943397	GM12878	blood:	n/a	n/a
39	EP300	chr3:97951405-97951686	GM12878	blood:	n/a	n/a
40	FOS	chr3:97928334-97928502	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr3:97942825-97942886	MCF10A-Er-Src	breast:	n/a	chr3:97942875-97942883 chr3:97942876-97942883 chr3:97942875-97942884 chr3:97942874-97942883
42	FOS	chr3:97945322-97945450	MCF10A-Er-Src	breast:	n/a	n/a
43	IKZF1	chr3:97952407-97952731	GM12878	blood:	n/a	n/a
44	JUN	chr3:97928145-97928303	HepG2	liver:	n/a	chr3:97928270-97928279 chr3:97928270-97928280 chr3:97928271-97928279 chr3:97928272-97928279 chr3:97928271-97928280
45	JUND	chr3:97928111-97928434	HepG2	liver:	n/a	chr3:97928270-97928279 chr3:97928270-97928280 chr3:97928271-97928279 chr3:97928272-97928279 chr3:97928271-97928280 chr3:97928269-97928280
46	MAFK	chr3:97937766-97937953	IMR90	lung:	n/a	n/a
47	MAX	chr3:97952237-97952646	GM12878	blood:	n/a	n/a
48	MAX	chr3:97950305-97950329	GM12878	blood:	n/a	n/a
49	MAZ	chr3:97934266-97934355	HepG2	liver:	n/a	n/a
50	MXI1	chr3:97952265-97952626	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MINA-2	chr3:97954345-97954692	XLOC_003187
2	lnc-MINA-2	chr3:97956121-97956219	XLOC_003187
3	lnc-MINA-2	chr3:97955718-97955882	XLOC_003187
4	lnc-MINA-2	chr3:97956121-97956211	XLOC_003187
5	lnc-MINA-2	chr3:97955718-97955882	XLOC_003187
6	lnc-MINA-2	chr3:97954530-97954692	XLOC_003187
7	lnc-MINA-2	chr3:97949910-97950089	XLOC_003187
8	lnc-MINA-2	chr3:97949910-97950089	XLOC_003187
9	lnc-MINA-2	chr3:97955718-97955882	XLOC_003187
10	lnc-MINA-2	chr3:97956121-97956217	XLOC_003187
11	lnc-MINA-6	chr3:97925331-97925450	NONHSAT090787
12	lnc-OR5H6-1	chr3:97952495-97952520	ENSG00000251088.1

Variant related genes	Relation type
OR5H3P	TF binding region
ENSG00000251088	TF binding region
OR5H7P	TF binding region
OR5H4P	TF binding region
POU2F1	miRNA target sites

Extended variants
information (count: 1327 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:1327 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1024055	chr3:97924688-97924689	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs563204136	chr3:97924689-97924690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs575321772	chr3:97924697-97924698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs115972782	chr3:97924712-97924713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs182767453	chr3:97924732-97924733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs150086075	chr3:97924777-97924778	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs115513201	chr3:97924798-97924799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs529844469	chr3:97924802-97924803	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs116058493	chr3:97924842-97924843	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs547568249	chr3:97924861-97924862	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs570598177	chr3:97924870-97924871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs76165502	chr3:97924871-97924872	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs556139421	chr3:97924958-97924959	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs569635925	chr3:97924983-97924984	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs75823195	chr3:97925074-97925075	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs554978157	chr3:97925109-97925110	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs2270675	chr3:97925124-97925125	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs79620787	chr3:97925126-97925127	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs565700414	chr3:97925147-97925148	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs1024056	chr3:97925202-97925203	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs142473990	chr3:97925205-97925206	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs565561166	chr3:97925221-97925222	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs577324961	chr3:97925239-97925240	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs151296337	chr3:97925254-97925255	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs190795933	chr3:97925262-97925263	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs140572742	chr3:97925265-97925266	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs116835153	chr3:97925266-97925267	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs562113795	chr3:97925271-97925272	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs149503103	chr3:97925279-97925280	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs369859552	chr3:97925288-97925289	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs371914977	chr3:97925308-97925309	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs77219277	chr3:97925317-97925318	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs145446224	chr3:97925336-97925337	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs570928238	chr3:97925376-97925377	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs568592518	chr3:97925388-97925389	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs78146469	chr3:97925389-97925390	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs549963409	chr3:97925413-97925414	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs114024455	chr3:97925416-97925417	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs535387501	chr3:97925451-97925452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs374938456	chr3:97925468-97925469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs183654561	chr3:97925480-97925481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs554520718	chr3:97925545-97925546	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs565376391	chr3:97925559-97925560	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs576332649	chr3:97925582-97925583	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs534618553	chr3:97925611-97925612	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs543003470	chr3:97925702-97925703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs188782780	chr3:97925726-97925727	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs7634735	chr3:97925727-97925728	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs546043710	chr3:97925741-97925742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs556826559	chr3:97925742-97925743	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

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
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:97917800-97927600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:97923600-97927600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:97926400-97926600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:97926600-97927600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:97927600-97927800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:97927600-97928200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:97927600-97928400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:97927600-97928800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr3:97927600-97928800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:97927800-97928200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:97928200-97928400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:97928200-97932200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:97928200-97936800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:97928400-97932200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:97928800-97931000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:97928800-97934000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:97930000-97932000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:97931000-97932800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:97931800-97932000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr3:97932000-97932200	Active TSS	H1 Cell Line	embryonic stem cell
21	chr3:97932000-97932200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:97932000-97932800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:97932200-97932600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
24	chr3:97932200-97932600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr3:97932200-97932600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr3:97932200-97932600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:97932200-97932800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr3:97932600-97932800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:97932600-97932800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr3:97932600-97933800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr3:97932800-97933600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:97932800-97933800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:97932800-97936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:97933800-97934000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr3:97933800-97934200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:97933800-97938000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:97934000-97934400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:97936200-97936800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr3:97936800-97937600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:97936800-97937800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:97937600-97938000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr3:97937800-97942400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:97938000-97938200	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:97942400-97943400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:97943400-97944000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:97944000-97944200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:97945200-97945600	Active TSS	Esophagus	oesophagus
48	chr3:97951200-97952800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:97951400-97952200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:97951600-97952800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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