Variant report

Variant	esv6955
Chromosome Location	chr5:100239361-100239554
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	ATF2	chr5:100238690-100240555	GM12878	blood:	n/a	n/a
2	ATF2	chr5:100238750-100239738	GM12878	blood:	n/a	n/a
3	BATF	chr5:100239024-100239641	GM12878	blood:	n/a	n/a
4	BCL3	chr5:100239329-100239646	GM12878	blood:	n/a	n/a
5	BCLAF1	chr5:100238723-100239804	GM12878	blood:	n/a	chr5:100239046-100239055
6	BCLAF1	chr5:100238657-100239850	GM12878	blood:	n/a	chr5:100239046-100239055
7	BHLHE40	chr5:100238806-100240722	GM12878	blood:	n/a	n/a
8	CEBPB	chr5:100238644-100239842	GM12878	blood:	n/a	chr5:100239027-100239035
9	CHD1	chr5:100234019-100241405	GM12878	blood:	n/a	n/a
10	CHD2	chr5:100237641-100239695	GM12878	blood:	n/a	n/a
11	CREB1	chr5:100238710-100240519	GM12878	blood:	n/a	n/a
12	CTBP2	chr5:100238226-100239563	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr5:100238763-100239429	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr5:100238192-100239491	H1-hESC	embryonic stem cell:	n/a	n/a
15	EBF1	chr5:100239023-100239363	GM12878	blood:	n/a	chr5:100239208-100239219
16	EBF1	chr5:100237565-100240618	GM12878	blood:	n/a	chr5:100239208-100239219
17	EGR1	chr5:100239314-100239596	GM12878	blood:	n/a	chr5:100239444-100239458 chr5:100239443-100239456 chr5:100239443-100239456 chr5:100239443-100239456 chr5:100239442-100239457 chr5:100239446-100239455 chr5:100239443-100239457 chr5:100239445-100239455 chr5:100239443-100239456
18	EGR1	chr5:100239303-100239539	GM12878	blood:	n/a	chr5:100239444-100239458 chr5:100239443-100239456 chr5:100239443-100239456 chr5:100239443-100239456 chr5:100239442-100239457 chr5:100239446-100239455 chr5:100239443-100239457 chr5:100239445-100239455 chr5:100239443-100239456
19	EGR1	chr5:100239323-100239558	K562	blood:	n/a	chr5:100239444-100239458 chr5:100239443-100239456 chr5:100239443-100239456 chr5:100239443-100239456 chr5:100239442-100239457 chr5:100239446-100239455 chr5:100239443-100239457 chr5:100239445-100239455 chr5:100239443-100239456
20	EGR1	chr5:100239234-100239569	K562	blood:	n/a	chr5:100239444-100239458 chr5:100239443-100239456 chr5:100239443-100239456 chr5:100239443-100239456 chr5:100239442-100239457 chr5:100239446-100239455 chr5:100239443-100239457 chr5:100239445-100239455 chr5:100239443-100239456
21	ELF1	chr5:100238770-100239726	GM12878	blood:	n/a	n/a
22	ELK1	chr5:100238796-100240590	GM12878	blood:	n/a	chr5:100240273-100240282 chr5:100240273-100240282
23	EP300	chr5:100238812-100239543	GM12878	blood:	n/a	chr5:100239231-100239247
24	EP300	chr5:100238838-100239735	GM12878	blood:	n/a	chr5:100239231-100239247
25	EP300	chr5:100238807-100240534	GM12878	blood:	n/a	chr5:100239231-100239247 chr5:100240274-100240281 chr5:100240431-100240440 chr5:100240427-100240441
26	FOXM1	chr5:100238731-100240627	GM12878	blood:	n/a	chr5:100239487-100239495 chr5:100240588-100240596
27	FOXM1	chr5:100238598-100240641	GM12878	blood:	n/a	chr5:100239487-100239495 chr5:100240588-100240596
28	GATA1	chr5:100238669-100239470	PBDE	blood:	n/a	n/a
29	HA-E2F1	chr5:100238577-100239557	MCF-7	breast:	n/a	n/a
30	IRF4	chr5:100238902-100239480	GM12878	blood:	n/a	n/a
31	IRF4	chr5:100238847-100239466	GM12878	blood:	n/a	n/a
32	KAP1	chr5:100238824-100239392	U2OS	brain:	n/a	n/a
33	KAP1	chr5:100236638-100239452	HEK293	kidney:	n/a	n/a
34	MAX	chr5:100235818-100240545	GM12878	blood:	n/a	chr5:100236095-100236103 chr5:100236092-100236102
35	MAX	chr5:100238575-100239518	ECC-1	luminal epithelium:	n/a	n/a
36	MAX	chr5:100235635-100240554	NB4	blood:	n/a	chr5:100236095-100236103 chr5:100236092-100236102
37	MAX	chr5:100238720-100239392	A549	lung:	n/a	n/a
38	MAZ	chr5:100238705-100241432	GM12878	blood:	n/a	n/a
39	MTA3	chr5:100235381-100240793	GM12878	blood:	n/a	n/a
40	MTA3	chr5:100235718-100240515	GM12878	blood:	n/a	n/a
41	MXI1	chr5:100234124-100240505	GM12878	blood:	n/a	chr5:100236093-100236102
42	MYC	chr5:100235575-100240405	NB4	blood:	n/a	chr5:100236095-100236103 chr5:100236092-100236102
43	NFATC1	chr5:100238807-100239773	GM12878	blood:	n/a	n/a
44	NFATC1	chr5:100238872-100239699	GM12878	blood:	n/a	n/a
45	NFIC	chr5:100235562-100241309	GM12878	blood:	n/a	chr5:100236970-100236987
46	NFIC	chr5:100238701-100239626	GM12878	blood:	n/a	n/a
47	NFYB	chr5:100238630-100239412	K562	blood:	n/a	n/a
48	PAX5	chr5:100238702-100239493	GM12878	blood:	n/a	n/a
49	PML	chr5:100235583-100240737	GM12878	blood:	n/a	chr5:100240171-100240179
50	PML	chr5:100238746-100239562	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:100239319-100239369	SK-N-SH_RA	brain:	n/a
2	chr5:100239319-100239369	SK-N-SH_RA	brain:	n/a
3	chr5:100239529-100239579	HEEpiC	esophagus:	n/a
4	chr5:100239319-100239369	H1-hESC	embryonic stem cell:	embryo
5	chr5:100239529-100239579	MCF10A-Er-Src	breast:	n/a
6	chr5:100239319-100239369	GM12892	blood:	n/a
7	chr5:100239529-100239579	AG04450	lung:	fetal
8	chr5:100239319-100239369	HEEpiC	esophagus:	n/a
9	chr5:100239529-100239579	SAEC	small airway:	n/a
10	chr5:100239529-100239579	K562	blood:	n/a
11	chr5:100239319-100239369	PFSK-1	brain:	n/a
12	chr5:100239529-100239579	Hepatocyte	liver:	n/a
13	chr5:100239319-100239369	T-47D	breast:	n/a
14	chr5:100239319-100239369	HCM	heart:	n/a
15	chr5:100239529-100239579	HCPEpiC	choroid plexus:	n/a
16	chr5:100239319-100239369	SKMC	muscle:	n/a
17	chr5:100239529-100239579	AoSMC	blood vessel:	n/a
18	chr5:100239529-100239579	HAEpiC	amniotic membrane:	n/a
19	chr5:100239319-100239369	HCF	heart:	n/a
20	chr5:100239529-100239579	ProgFib	skin:	n/a
21	chr5:100239529-100239579	IMR90	lung:	fetal
22	chr5:100239319-100239369	CMK	blood:	n/a
23	chr5:100239529-100239579	SK-N-MC	brain:	n/a
24	chr5:100239529-100239579	LNCaP	prostate:	n/a
25	chr5:100239529-100239579	HepG2	liver:	n/a
26	chr5:100239529-100239579	HNPCEpiC	eye:	n/a
27	chr5:100239529-100239579	Caco-2	colon:	n/a
28	chr5:100239319-100239369	NB4	blood:	n/a
29	chr5:100239529-100239579	H1-hESC	embryonic stem cell:	embryo
30	chr5:100239319-100239369	HRCEpiC	kidney:	n/a
31	chr5:100239529-100239579	SK-N-SH_RA	brain:	n/a
32	chr5:100239529-100239579	U87	brain:	n/a
33	chr5:100239529-100239579	MCF-7	breast:	n/a
34	chr5:100239529-100239579	HPAEpiC	pulmonary alveolar:	n/a
35	chr5:100239319-100239369	BJ	skin:	n/a
36	chr5:100239529-100239579	GM06990	blood:	n/a
37	chr5:100239529-100239579	HUVEC	blood vessel:	n/a
38	chr5:100239319-100239369	HRE	kidney:	n/a
39	chr5:100239529-100239579	HCM	heart:	n/a
40	chr5:100239319-100239369	HMEC	breast:	n/a
41	chr5:100239529-100239579	GM19239	blood:	n/a
42	chr5:100239319-100239369	ECC-1	luminal epithelium:	n/a
43	chr5:100239319-100239369	GM19239	blood:	n/a
44	chr5:100239529-100239579	A549	lung:	n/a
45	chr5:100239319-100239369	HRPEpiC	eye:	n/a
46	chr5:100239319-100239369	AG04449	skin:	fetal
47	chr5:100239319-100239369	NHDF-neo	bronchial:	n/a
48	chr5:100239319-100239369	NHBE	bronchial:	n/a
49	chr5:100239529-100239579	HRE	kidney:	n/a
50	chr5:100239529-100239579	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100235471..100237177-chr5:100239022..100241293,2	MCF-7	breast:

Variant related genes	Relation type
ST8SIA4	TF binding region
ST8SIA4	CpG island

Extended variants
information (count: 6 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1292792	chr5:100239404-100239405	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs574968556	chr5:100239431-100239432	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs146646446	chr5:100239448-100239449	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs28644326	chr5:100239478-100239479	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs4146199	chr5:100239517-100239518	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs3756354	chr5:100239533-100239534	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:85)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Cancer	16751803	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
Non-small cell lung cancer	21829676	CNVD
adenomatous polyposis	22470819	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Urothelial carcinoma	21177765	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
Lung cancer	18438408	CNVD
Retinoblastoma	22278416	CNVD
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
Breast cancer	21785460	CNVD
Merkel cell carcinoma	19020549	CNVD
Squamous cell cancer	20885788	CNVD
Hepatocellular carcinoma	16750200	CNVD
Neurodevelopmental disorder	22521361	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	17133270	CNVD
Acute myeloid leukemia	20729466	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
lymphocytic leukemia	21291569	CNVD
Testicular cancer	18059402	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16573809	CNVD
Renal cell carcinoma	18194544	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Cancer	20164920	CNVD
Myelodysplastic syndrome	21251322	CNVD
abnormal development	18461090	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16774939	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Multiple myeloma	17550852	CNVD
Glioblastoma multiforme	22286061	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Ovarian cancer	21720365	CNVD
Prostate cancer	16461572	CNVD
Neurocytoma	17123091	CNVD
Salivary gland tumor	18059337	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:147 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100232600-100245600	Active TSS	GM12878-XiMat	blood
2	chr5:100235400-100241400	Active TSS	Duodenum Mucosa	Duodenum
3	chr5:100235600-100240400	Active TSS	Brain Angular Gyrus	brain
4	chr5:100235600-100240600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:100235600-100240600	Active TSS	Thymus	Thymus
6	chr5:100235800-100239600	Active TSS	HSMMtube	muscle
7	chr5:100235800-100239800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:100235800-100240400	Active TSS	Brain Anterior Caudate	brain
9	chr5:100235800-100240400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:100235800-100240400	Active TSS	Lung	lung
11	chr5:100235800-100240600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
12	chr5:100235800-100240600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:100235800-100241000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:100235800-100241400	Active TSS	Right Atrium	heart
15	chr5:100236000-100239400	Active TSS	Primary T cells from cord blood	blood
16	chr5:100236000-100239600	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr5:100236000-100239600	Active TSS	A549	lung
18	chr5:100236000-100239800	Active TSS	NHDF-Ad	bronchial
19	chr5:100236000-100240400	Active TSS	Colonic Mucosa	Colon
20	chr5:100236000-100240400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr5:100236000-100240400	Active TSS	Small Intestine	intestine
22	chr5:100236000-100240600	Active TSS	Right Ventricle	heart
23	chr5:100236000-100240600	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr5:100236000-100240800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:100236200-100239400	Active TSS	Primary monocytes fromperipheralblood	blood
26	chr5:100236200-100239600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:100236200-100239600	Active TSS	Fetal Lung	lung
28	chr5:100236200-100240800	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr5:100236200-100241200	Active TSS	Liver	Liver
30	chr5:100236200-100241400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr5:100236400-100239400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:100236600-100240800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:100237000-100239600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr5:100237000-100240400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
35	chr5:100237200-100239400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
36	chr5:100237200-100239600	Active TSS	Primary B cells from peripheral blood	blood
37	chr5:100237200-100239600	Active TSS	Placenta	Placenta
38	chr5:100237200-100239800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr5:100237200-100239800	Active TSS	Placenta Amnion	Placenta Amnion
40	chr5:100237200-100240000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr5:100237200-100240200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:100237200-100240400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:100237200-100240400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
44	chr5:100237200-100241000	Active TSS	Left Ventricle	heart
45	chr5:100237200-100241400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:100237400-100239400	Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr5:100237400-100239400	Active TSS	Primary T cells fromperipheralblood	blood
48	chr5:100237400-100239600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr5:100237400-100239600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:100237400-100239800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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