Variant report

Variant	esv3418530
Chromosome Location	chr9:140410431-140414529
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	ATF1	chr9:140413661-140413862	K562	blood:	n/a	n/a
2	ATF3	chr9:140412120-140413744	K562	blood:	n/a	n/a
3	ATF3	chr9:140411269-140411670	K562	blood:	n/a	n/a
4	ATF3	chr9:140411303-140411539	K562	blood:	n/a	n/a
5	BHLHE40	chr9:140413599-140414372	K562	blood:	n/a	n/a
6	CBX3	chr9:140413277-140413859	K562	blood:	n/a	n/a
7	CEBPB	chr9:140413462-140413696	IMR90	lung:	n/a	chr9:140413648-140413656
8	CEBPB	chr9:140413585-140413601	A549	lung:	n/a	n/a
9	E2F6	chr9:140413628-140413831	K562	blood:	n/a	n/a
10	EP300	chr9:140411532-140412646	GM12878	blood:	n/a	n/a
11	FOS	chr9:140413458-140413879	MCF10A-Er-Src	breast:	n/a	chr9:140413722-140413734 chr9:140413722-140413733 chr9:140413727-140413734 chr9:140413723-140413733 chr9:140413619-140413629 chr9:140413723-140413732
12	FOS	chr9:140413497-140413820	MCF10A-Er-Src	breast:	n/a	chr9:140413722-140413734 chr9:140413722-140413733 chr9:140413727-140413734 chr9:140413723-140413733 chr9:140413619-140413629 chr9:140413723-140413732
13	FOS	chr9:140413566-140413772	MCF10A-Er-Src	breast:	n/a	chr9:140413722-140413734 chr9:140413722-140413733 chr9:140413727-140413734 chr9:140413723-140413733 chr9:140413619-140413629 chr9:140413723-140413732
14	FOS	chr9:140413566-140413839	MCF10A-Er-Src	breast:	n/a	chr9:140413722-140413734 chr9:140413722-140413733 chr9:140413727-140413734 chr9:140413723-140413733 chr9:140413619-140413629 chr9:140413723-140413732
15	FOSL1	chr9:140413595-140413890	K562	blood:	n/a	chr9:140413722-140413734 chr9:140413722-140413733 chr9:140413722-140413733 chr9:140413727-140413734 chr9:140413723-140413733 chr9:140413619-140413629 chr9:140413723-140413732
16	FOSL1	chr9:140413505-140414000	K562	blood:	n/a	chr9:140413722-140413734 chr9:140413722-140413733 chr9:140413722-140413733 chr9:140413727-140413734 chr9:140413723-140413733 chr9:140413619-140413629 chr9:140413723-140413732
17	FOSL2	chr9:140411448-140412672	HepG2	liver:	n/a	n/a
18	GABPA	chr9:140411788-140412321	Hela-S3	cervix:	n/a	n/a
19	GABPA	chr9:140411377-140413301	Hela-S3	cervix:	n/a	n/a
20	GABPA	chr9:140412432-140412576	Hela-S3	cervix:	n/a	n/a
21	GABPA	chr9:140411555-140411766	Hela-S3	cervix:	n/a	n/a
22	GATA2	chr9:140411388-140412266	K562	blood:	n/a	n/a
23	HEY1	chr9:140411460-140412407	K562	blood:	n/a	n/a
24	IRF4	chr9:140411382-140412729	GM12878	blood:	n/a	n/a
25	JUND	chr9:140413612-140413788	HepG2	liver:	n/a	chr9:140413722-140413734 chr9:140413722-140413733 chr9:140413727-140413734 chr9:140413723-140413733 chr9:140413619-140413629 chr9:140413723-140413732
26	JUND	chr9:140413572-140413909	K562	blood:	n/a	chr9:140413722-140413734 chr9:140413722-140413733 chr9:140413727-140413734 chr9:140413723-140413733 chr9:140413619-140413629 chr9:140413723-140413732
27	MAX	chr9:140413531-140414243	K562	blood:	n/a	chr9:140413724-140413733
28	MEF2A	chr9:140413455-140413788	K562	blood:	n/a	chr9:140413653-140413667 chr9:140413652-140413667 chr9:140413654-140413665 chr9:140413653-140413668 chr9:140413652-140413667 chr9:140413655-140413666 chr9:140413651-140413667 chr9:140413655-140413664 chr9:140413648-140413669 chr9:140413724-140413732 chr9:140413652-140413668 chr9:140413648-140413669
29	MYC	chr9:140410958-140411258	MCF10A-Er-Src	breast:	n/a	n/a
30	MYC	chr9:140413596-140413757	MCF10A-Er-Src	breast:	n/a	chr9:140413724-140413733
31	PAX5	chr9:140411321-140412549	GM12878	blood:	n/a	n/a
32	PAX5	chr9:140411433-140412459	GM12878	blood:	n/a	n/a
33	POU2F2	chr9:140411330-140413470	GM12891	blood:	n/a	n/a
34	POU2F2	chr9:140411493-140411769	GM12878	blood:	n/a	n/a
35	POU2F2	chr9:140411830-140412178	GM12878	blood:	n/a	n/a
36	POU2F2	chr9:140411302-140413573	GM12891	blood:	n/a	n/a
37	POU2F2	chr9:140411309-140413607	GM12878	blood:	n/a	n/a
38	POU2F2	chr9:140412302-140412471	GM12878	blood:	n/a	n/a
39	RCOR1	chr9:140413678-140413732	K562	blood:	n/a	n/a
40	REST	chr9:140411454-140412729	PANC-1	pancreas:	n/a	n/a
41	SIN3AK20	chr9:140411609-140411713	HepG2	liver:	n/a	n/a
42	SIX5	chr9:140411501-140411734	K562	blood:	n/a	n/a
43	SIX5	chr9:140413042-140413283	K562	blood:	n/a	n/a
44	SIX5	chr9:140411764-140412246	K562	blood:	n/a	n/a
45	SP1	chr9:140411755-140412205	GM12878	blood:	n/a	n/a
46	SPI1	chr9:140411751-140412144	K562	blood:	n/a	n/a
47	STAT3	chr9:140410770-140410887	MCF10A-Er-Src	breast:	n/a	n/a
48	TAF1	chr9:140411490-140412275	HepG2	liver:	n/a	n/a
49	TBP	chr9:140410587-140410814	H1-hESC	embryonic stem cell:	n/a	n/a
50	ZBTB33	chr9:140411788-140412085	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:140352371..140354173-chr9:140410410..140412850,2	MCF-7	breast:
2	chr9:140385602..140387946-chr9:140412336..140414686,2	K562	blood:
3	chr9:140192004..140196032-chr9:140413457..140417425,3	MCF-7	breast:
4	chr9:140412465..140415104-chr9:140500104..140501750,2	MCF-7	breast:
5	chr9:140407045..140410269-chr9:140412474..140414794,3	MCF-7	breast:
6	chr9:140189647..140191629-chr9:140408835..140411014,2	MCF-7	breast:
7	chr9:140413558..140415139-chr9:140438109..140439773,2	MCF-7	breast:
8	chr9:140414414..140417043-chr9:140441258..140443009,2	MCF-7	breast:
9	chr9:140408886..140411394-chr9:140412638..140414476,2	MCF-7	breast:
10	chr9:140199124..140201769-chr9:140410590..140413646,3	K562	blood:
11	chr9:140414450..140416350-chr9:140433102..140436050,2	MCF-7	breast:
12	chr9:140332776..140334313-chr9:140412829..140415749,2	MCF-7	breast:
13	chr9:140386446..140388269-chr9:140413186..140415741,2	K562	blood:
14	chr9:140412905..140414820-chr9:140475554..140478292,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR85-1	chr9:140411319-140412418	NONHSAT135734
2	lnc-WDR85-1	chr9:140412889-140412899	NONHSAT135734

Variant related genes	Relation type
PNPLA7	TF binding region
ENSG00000130653	chromatin interactions
ENSG00000165802	chromatin interactions
ENSG00000197070	chromatin interactions
ENSG00000260996	chromatin interactions

Extended variants
information (count: 229 )
Associated
traits (count: 20 )

Variant overlapped rSNPs/rCNVs (count:229 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs576678215	chr9:140410527-140410528	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs536072530	chr9:140410536-140410537	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs554349175	chr9:140410537-140410538	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs574514184	chr9:140410546-140410547	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs184303992	chr9:140410554-140410555	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs539842707	chr9:140410564-140410565	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs883702	chr9:140410589-140410590	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs148681782	chr9:140410619-140410620	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs375470563	chr9:140410662-140410663	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs545658070	chr9:140410689-140410690	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs544633293	chr9:140410711-140410712	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs188044187	chr9:140410720-140410721	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs192322338	chr9:140410736-140410737	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs542043657	chr9:140410740-140410741	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs558629466	chr9:140410754-140410755	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs185515555	chr9:140410761-140410762	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs544056679	chr9:140410765-140410766	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs570822534	chr9:140410771-140410772	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs533383211	chr9:140410787-140410788	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs550471924	chr9:140410788-140410789	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs550414862	chr9:140410799-140410800	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs563855840	chr9:140410860-140410861	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs570358847	chr9:140410865-140410866	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs2480105	chr9:140410881-140410882	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs555972345	chr9:140410906-140410907	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs543324518	chr9:140410959-140410960	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs566143738	chr9:140410990-140410991	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs372601263	chr9:140411001-140411002	Weak transcription Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs553466485	chr9:140411069-140411070	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs576402084	chr9:140411077-140411078	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs377077188	chr9:140411142-140411143	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs75806404	chr9:140411174-140411175	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs118009646	chr9:140411272-140411273	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs539171251	chr9:140411285-140411286	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs79164050	chr9:140411288-140411289	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs541657343	chr9:140411330-140411331	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
37	rs189384237	chr9:140411349-140411350	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
38	rs147413148	chr9:140411387-140411388	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
39	rs541506151	chr9:140411396-140411397	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
40	rs139663472	chr9:140411410-140411411	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
41	rs201015770	chr9:140411431-140411432	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
42	rs76545475	chr9:140411440-140411441	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
43	rs200500975	chr9:140411459-140411460	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs550236558	chr9:140411460-140411461	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
45	rs71829372	chr9:140411461-140411462	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
46	rs570248724	chr9:140411463-140411464	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
47	rs529542478	chr9:140411487-140411488	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
48	rs372512665	chr9:140411490-140411491	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
49	rs549420874	chr9:140411539-140411540	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
50	rs371007805	chr9:140411660-140411661	Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:20)

Disease	PMID	Source
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Cardiac fibroma	18329553	CNVD
Lung cancer	19147751	CNVD
Cervical cancer	17311676	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastric cancer	17908304	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Chordoma	18071362	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Sudden cardiac death	19188705	CNVD
Myoepithelioma	18604193	CNVD
Tuberous sclerosis	19566914	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Mantle cell lymphoma	19029149	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140376800-140444000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:140377000-140437000	Weak transcription	Left Ventricle	heart
3	chr9:140377200-140420200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:140388400-140425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:140392000-140425800	Weak transcription	Primary T cells from cord blood	blood
6	chr9:140393000-140417800	Weak transcription	Fetal Brain Female	brain
7	chr9:140393000-140429400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:140394000-140419800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr9:140394000-140429200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:140394800-140415600	Weak transcription	Brain Angular Gyrus	brain
11	chr9:140395000-140414000	Weak transcription	Brain Substantia Nigra	brain
12	chr9:140396400-140429200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:140401400-140413600	Weak transcription	Gastric	stomach
14	chr9:140404000-140413400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:140404200-140413800	Weak transcription	Primary B cells from cord blood	blood
16	chr9:140404200-140414000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:140404200-140414000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:140404200-140415000	Weak transcription	HSMMtube	muscle
19	chr9:140404200-140415600	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:140404200-140420000	Weak transcription	Brain Anterior Caudate	brain
21	chr9:140404200-140429200	Weak transcription	Aorta	Aorta
22	chr9:140404400-140415600	Weak transcription	Lung	lung
23	chr9:140406000-140413800	Weak transcription	Fetal Intestine Small	intestine
24	chr9:140406800-140420000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:140407000-140413600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:140407000-140414000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:140407200-140413400	Weak transcription	K562	blood
28	chr9:140407200-140414000	Weak transcription	Liver	Liver
29	chr9:140407200-140414000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:140408600-140410600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:140408600-140410600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:140408600-140413800	Weak transcription	Colonic Mucosa	Colon
33	chr9:140408600-140444400	Weak transcription	Esophagus	oesophagus
34	chr9:140409000-140413400	Weak transcription	Osteobl	bone
35	chr9:140409200-140410800	Strong transcription	Ovary	ovary
36	chr9:140409400-140411000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:140409800-140420000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:140410000-140410600	Weak transcription	Spleen	Spleen
39	chr9:140410000-140413400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:140410000-140413800	Weak transcription	Adipose Nuclei	Adipose
41	chr9:140410000-140413800	Weak transcription	Fetal Stomach	stomach
42	chr9:140410000-140427200	Weak transcription	Stomach Mucosa	stomach
43	chr9:140410000-140429200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:140410200-140413800	Weak transcription	Pancreas	Pancrea
45	chr9:140410200-140414200	Weak transcription	Right Ventricle	heart
46	chr9:140410200-140418400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr9:140410400-140410600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:140410400-140411200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:140410400-140412000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:140410600-140410800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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