Variant report

Variant	rs1531063
Chromosome Location	chr19:41225319-41225320
allele	C/T
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	MAX	chr19:41220113-41225416	A549	lung:	n/a	chr19:41225122-41225132 chr19:41222713-41222723 chr19:41222082-41222091
2	BCL3	chr19:41220248-41225401	A549	lung:	n/a	chr19:41225228-41225237 chr19:41222875-41222884 chr19:41222082-41222091 chr19:41222234-41222243
3	POLR2A	chr19:41220316-41225389	H1-hESC	embryonic stem cell:	n/a	n/a
4	EBF1	chr19:41224880-41225643	GM12878	blood:	n/a	chr19:41225188-41225199
5	MAX	chr19:41224676-41225390	HepG2	liver:	n/a	chr19:41225122-41225132
6	MYC	chr19:41224871-41225334	MCF10A-Er-Src	breast:	n/a	chr19:41225122-41225132
7	ZNF384	chr19:41225220-41225550	K562	blood:	n/a	n/a
8	EP300	chr19:41224982-41225397	GM12878	blood:	n/a	n/a
9	E2F6	chr19:41224348-41225436	A549	lung:	n/a	chr19:41224924-41224936
10	PAX5	chr19:41225267-41225522	GM12878	blood:	n/a	n/a
11	EBF1	chr19:41224779-41225444	GM12878	blood:	n/a	chr19:41225188-41225199
12	REST	chr19:41223166-41225339	A549	lung:	n/a	n/a
13	POLR2A	chr19:41224775-41225346	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr19:41220314-41228780	MCF10A-Er-Src	breast:	n/a	n/a
15	RAD21	chr19:41224896-41225401	Hela-S3	cervix:	n/a	n/a
16	PAX5	chr19:41225196-41225742	GM12878	blood:	n/a	chr19:41225228-41225237
17	MAX	chr19:41224746-41225352	SK-N-SH	brain:	n/a	chr19:41225122-41225132
18	POLR2A	chr19:41220376-41228744	MCF10A-Er-Src	breast:	n/a	n/a
19	MXI1	chr19:41224831-41225398	GM12878	blood:	n/a	n/a
20	MXI1	chr19:41220156-41225428	IMR90	lung:	n/a	n/a
21	POLR2A	chr19:41224125-41225805	HepG2	liver:	n/a	n/a
22	PAX5	chr19:41225292-41225631	GM12878	blood:	n/a	n/a
23	FOS	chr19:41224830-41225366	MCF10A-Er-Src	breast:	n/a	chr19:41225230-41225239
24	MAX	chr19:41220045-41225483	A549	lung:	n/a	chr19:41225122-41225132 chr19:41222713-41222723 chr19:41222082-41222091
25	STAT3	chr19:41225123-41225374	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr19:41224787-41225454	HUVEC	blood vessel:	n/a	n/a
27	PML	chr19:41224828-41225424	GM12878	blood:	n/a	n/a
28	MAX	chr19:41224646-41225339	ECC-1	luminal epithelium:	n/a	chr19:41225122-41225132
29	NFIC	chr19:41224630-41225356	ECC-1	luminal epithelium:	n/a	n/a
30	MYBL2	chr19:41224703-41225319	HepG2	liver:	n/a	n/a
31	POLR2A	chr19:41224277-41225343	HUVEC	blood vessel:	n/a	n/a
32	EP300	chr19:41224459-41225345	ECC-1	luminal epithelium:	n/a	chr19:41224842-41224852
33	SIN3AK20	chr19:41220582-41225437	MCF-7	breast:	n/a	n/a
34	FOS	chr19:41224897-41225325	MCF10A-Er-Src	breast:	n/a	chr19:41225230-41225239
35	MAX	chr19:41224810-41225349	GM12878	blood:	n/a	chr19:41225122-41225132
36	MAZ	chr19:41224936-41225391	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:41224297-41225333	HCT-116	colon:	n/a	n/a
38	REST	chr19:41224875-41225391	MCF-7	breast:	n/a	n/a
39	POLR2A	chr19:41224797-41225340	GM12892	blood:	n/a	n/a
40	TCF12	chr19:41220164-41225474	A549	lung:	n/a	chr19:41221137-41221145
41	USF1	chr19:41224657-41225353	HCT-116	colon:	n/a	n/a
42	MAX	chr19:41224335-41225428	HepG2	liver:	n/a	chr19:41225122-41225132
43	RUNX3	chr19:41225220-41225750	GM12878	blood:	n/a	n/a
44	JUN	chr19:41220892-41225445	K562	blood:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222081-41222091 chr19:41225230-41225239 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222917-41222926 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
45	SIN3AK20	chr19:41224443-41225391	MCF-7	breast:	n/a	n/a
46	POLR2A	chr19:41220550-41225352	IMR90	lung:	n/a	n/a
47	MAX	chr19:41224652-41225338	ECC-1	luminal epithelium:	n/a	chr19:41225122-41225132
48	MAX	chr19:41224587-41225418	HCT-116	colon:	n/a	chr19:41225122-41225132
49	MAX	chr19:41224622-41225386	MCF-7	breast:	n/a	chr19:41225122-41225132
50	ZNF143	chr19:41224919-41225371	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41224831..41226803-chr19:41249457..41251875,2	K562	blood:
2	chr19:41224824..41227088-chr19:41310622..41313092,2	MCF-7	breast:
3	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
4	chr19:41225203..41228152-chr19:41229042..41232599,3	MCF-7	breast:
5	chr19:41224337..41226397-chr19:41306033..41307626,2	K562	blood:
6	chr19:41193561..41199772-chr19:41221208..41225709,11	K562	blood:
7	chr19:41224377..41227042-chr19:41281377..41283783,3	MCF-7	breast:
8	chr19:41224564..41226766-chr3:161088576..161090786,2	MCF-7	breast:
9	chr19:41224657..41226437-chr19:41266206..41269077,2	MCF-7	breast:
10	chr19:41194805..41199772-chr19:41221674..41225965,11	K562	blood:
11	chr19:41225224..41227952-chr19:41245122..41248446,3	MCF-7	breast:
12	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
13	chr19:41205738..41209357-chr19:41220858..41225801,5	MCF-7	breast:
14	chr19:41224979..41226592-chr19:41227722..41229766,2	K562	blood:
15	chr19:41224721..41227148-chr19:41302837..41304471,2	K562	blood:
16	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
17	chr19:41224929..41227139-chr19:41232897..41235326,2	K562	blood:
18	chr19:41220057..41225402-chr19:41302090..41307926,9	MCF-7	breast:
19	chr19:14628666..14629338-chr19:41224844..41225838,2	Hela-S3	cervix:
20	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
21	chr19:41223813..41226637-chr19:41310296..41313871,3	MCF-7	breast:
22	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
23	chr19:41116192..41118277-chr19:41225269..41226829,2	MCF-7	breast:
24	chr19:41225019..41226612-chr19:41226846..41228411,3	MCF-7	breast:
25	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
26	chr19:41223981..41226562-chr19:41304181..41307698,5	MCF-7	breast:
27	chr19:41224545..41226553-chr19:41238187..41240048,2	MCF-7	breast:

Variant related genes	Relation type
ADCK4	TF binding region
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000132002	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000261857	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10420651	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10420685	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1455434	0.81[EUR][1000 genomes]
rs1869710	0.81[EUR][1000 genomes]
rs2254326	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2254338	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2303723	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2561529	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2561531	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2607418	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34633896	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745212	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7250888	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41220400-41225400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:41220400-41225600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr19:41220400-41225800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:41220400-41226800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr19:41220600-41225400	Active TSS	Left Ventricle	heart
6	chr19:41220600-41225400	Active TSS	Psoas Muscle	Psoas
7	chr19:41220600-41225600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:41220600-41225600	Active TSS	Aorta	Aorta
9	chr19:41220600-41225800	Active TSS	Gastric	stomach
10	chr19:41220600-41226400	Active TSS	Right Atrium	heart
11	chr19:41220600-41227000	Active TSS	Esophagus	oesophagus
12	chr19:41220800-41226200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:41221400-41226200	Active TSS	HMEC	breast
14	chr19:41221600-41225400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:41221600-41225600	Active TSS	NHEK	skin
16	chr19:41221600-41226400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr19:41221800-41225600	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr19:41221800-41225800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr19:41222200-41225600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:41222200-41225600	Active TSS	Small Intestine	intestine
21	chr19:41222200-41225800	Active TSS	Placenta Amnion	Placenta Amnion
22	chr19:41222200-41226000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:41222400-41225400	Active TSS	Fetal Intestine Large	intestine
24	chr19:41222400-41225400	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr19:41222400-41225600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:41222400-41225600	Active TSS	Pancreas	Pancrea
27	chr19:41222400-41226800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:41222400-41227000	Active TSS	Lung	lung
29	chr19:41222600-41225400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:41222600-41225400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr19:41222600-41225400	Active TSS	Fetal Kidney	kidney
32	chr19:41222600-41225600	Active TSS	NHDF-Ad	bronchial
33	chr19:41222600-41225800	Active TSS	NHLF	lung
34	chr19:41222600-41226200	Active TSS	HSMMtube	muscle
35	chr19:41223200-41225600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:41223200-41225800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:41223400-41225400	Flanking Active TSS	Thymus	Thymus
38	chr19:41223400-41225600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr19:41223400-41225600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr19:41223400-41225600	Flanking Active TSS	Fetal Muscle Trunk	muscle
41	chr19:41223400-41225800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:41223400-41225800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr19:41223400-41225800	Flanking Active TSS	Liver	Liver
44	chr19:41223400-41225800	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr19:41223400-41225800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr19:41223400-41225800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr19:41223400-41226000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr19:41223400-41226800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr19:41223400-41227200	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr19:41223400-41227200	Flanking Active TSS	HUVEC	blood vessel

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