Variant report

Variant	rs2561530
Chromosome Location	chr19:41224314-41224315
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	CHD2	chr19:41224203-41224359	HepG2	liver:	n/a	n/a
4	MAFK	chr19:41223800-41224314	IMR90	lung:	n/a	chr19:41223967-41223982
5	WRNIP1	chr19:41224285-41224485	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:41220316-41225389	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIX5	chr19:41224092-41225211	A549	lung:	n/a	n/a
8	FOXA2	chr19:41224232-41225184	A549	lung:	n/a	n/a
9	SIN3A	chr19:41220570-41224559	H1-hESC	embryonic stem cell:	n/a	chr19:41222914-41222925
10	REST	chr19:41223166-41225339	A549	lung:	n/a	n/a
11	POLR2A	chr19:41220314-41228780	MCF10A-Er-Src	breast:	n/a	n/a
12	SIN3AK20	chr19:41220499-41225010	A549	lung:	n/a	n/a
13	POLR2A	chr19:41220376-41228744	MCF10A-Er-Src	breast:	n/a	n/a
14	MXI1	chr19:41220156-41225428	IMR90	lung:	n/a	n/a
15	REST	chr19:41224212-41224836	A549	lung:	n/a	n/a
16	MAFK	chr19:41223346-41224351	Hela-S3	cervix:	n/a	chr19:41223967-41223982
17	POLR2A	chr19:41224125-41225805	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:41220722-41224355	H1-hESC	embryonic stem cell:	n/a	n/a
19	EGR1	chr19:41223955-41224358	K562	blood:	n/a	n/a
20	MAX	chr19:41220045-41225483	A549	lung:	n/a	chr19:41225122-41225132 chr19:41222713-41222723 chr19:41222082-41222091
21	SMARCC1	chr19:41223417-41225230	Hela-S3	cervix:	n/a	n/a
22	MAX	chr19:41224305-41225272	Hela-S3	cervix:	n/a	chr19:41225122-41225132
23	MAZ	chr19:41223997-41224355	K562	blood:	n/a	n/a
24	SIN3AK20	chr19:41224062-41224667	K562	blood:	n/a	n/a
25	EP300	chr19:41223996-41225151	A549	lung:	n/a	chr19:41224842-41224852
26	POLR2A	chr19:41224277-41225343	HUVEC	blood vessel:	n/a	n/a
27	SIN3AK20	chr19:41220582-41225437	MCF-7	breast:	n/a	n/a
28	POLR2A	chr19:41223747-41224321	A549	lung:	n/a	n/a
29	CREB1	chr19:41223905-41224603	A549	lung:	n/a	n/a
30	POLR2A	chr19:41223829-41224322	MCF-7	breast:	n/a	n/a
31	ELK1	chr19:41224156-41224446	K562	blood:	n/a	n/a
32	POLR2A	chr19:41224297-41225333	HCT-116	colon:	n/a	n/a
33	TBL1XR1	chr19:41224206-41224497	K562	blood:	n/a	n/a
34	POLR2A	chr19:41224263-41224340	K562	blood:	n/a	n/a
35	TCF12	chr19:41220164-41225474	A549	lung:	n/a	chr19:41221137-41221145
36	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
37	ZNF263	chr19:41224118-41225186	HEK293-T-REx	kidney:	n/a	chr19:41224392-41224413 chr19:41224336-41224345
38	POLR2A	chr19:41220550-41225352	IMR90	lung:	n/a	n/a
39	UBTF	chr19:41222714-41225147	K562	blood:	n/a	n/a
40	FOSL2	chr19:41220277-41224942	A549	lung:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222917-41222926 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
41	POLR2A	chr19:41220983-41225287	HepG2	liver:	n/a	n/a
42	MAZ	chr19:41220232-41225451	IMR90	lung:	n/a	chr19:41222713-41222723 chr19:41222082-41222091
43	SIN3AK20	chr19:41223156-41224689	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41222253..41224407-chr19:41315424..41318276,2	K562	blood:
2	chr19:41113914..41116044-chr19:41221538..41224427,3	MCF-7	breast:
3	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
4	chr19:41220938..41225137-chr19:41311275..41314518,5	K562	blood:
5	chr19:41220005..41225073-chr19:41230462..41235365,8	K562	blood:
6	chr19:41193561..41199772-chr19:41221208..41225709,11	K562	blood:
7	chr19:41207302..41211180-chr19:41220761..41224340,7	K562	blood:
8	chr19:41194805..41199772-chr19:41221674..41225965,11	K562	blood:
9	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
10	chr19:41205738..41209357-chr19:41220858..41225801,5	MCF-7	breast:
11	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
12	chr19:41220057..41225402-chr19:41302090..41307926,9	MCF-7	breast:
13	chr19:40971240..40973961-chr19:41221836..41225167,3	MCF-7	breast:
14	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
15	chr19:41223813..41226637-chr19:41310296..41313871,3	MCF-7	breast:
16	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
17	chr19:41220720..41224635-chr19:41312175..41316788,5	MCF-7	breast:
18	chr19:41193720..41198590-chr19:41218677..41224410,19	MCF-7	breast:
19	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
20	chr19:41223981..41226562-chr19:41304181..41307698,5	MCF-7	breast:
21	chr19:41221142..41224353-chr19:41311383..41314668,3	K562	blood:

Variant related genes	Relation type
ADCK4	TF binding region
ENSG00000123815	Chromatin interaction
ENSG00000090013	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000233622	Chromatin interaction
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11538385	0.81[GIH][hapmap];0.82[JPT][hapmap]
rs11672197	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2561528	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2604888	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2604913	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs3865451	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs3865452	0.83[GIH][hapmap]

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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2561530	IRF2BP1	cis	parietal	SCAN
rs2561530	LIN7B	cis	parietal	SCAN
rs2561530	C19orf54	Cis_1M	lymphoblastoid	RTeQTL
rs2561530	KCNN4	cis	cerebellum	SCAN
rs2561530	BCAT2	cis	cerebellum	SCAN
rs2561530	APOC4	cis	cerebellum	SCAN
rs2561530	C19orf54	cis	lymphoblastoid	seeQTL

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	chr19:41220600-41224800	Active TSS	Right Ventricle	heart
6	chr19:41220600-41225200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:41220600-41225400	Active TSS	Left Ventricle	heart
8	chr19:41220600-41225400	Active TSS	Psoas Muscle	Psoas
9	chr19:41220600-41225600	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:41220600-41225600	Active TSS	Aorta	Aorta
11	chr19:41220600-41225800	Active TSS	Gastric	stomach
12	chr19:41220600-41226400	Active TSS	Right Atrium	heart
13	chr19:41220600-41227000	Active TSS	Esophagus	oesophagus
14	chr19:41220800-41226200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:41221000-41225200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr19:41221400-41226200	Active TSS	HMEC	breast
17	chr19:41221600-41225200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:41221600-41225400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr19:41221600-41225600	Active TSS	NHEK	skin
20	chr19:41221600-41226400	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr19:41221800-41225600	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:41221800-41225800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr19:41222000-41225000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr19:41222200-41225000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:41222200-41225000	Active TSS	Ovary	ovary
26	chr19:41222200-41225200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr19:41222200-41225600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:41222200-41225600	Active TSS	Small Intestine	intestine
29	chr19:41222200-41225800	Active TSS	Placenta Amnion	Placenta Amnion
30	chr19:41222200-41226000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr19:41222400-41224800	Bivalent/Poised TSS	HepG2	liver
32	chr19:41222400-41225200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:41222400-41225400	Active TSS	Fetal Intestine Large	intestine
34	chr19:41222400-41225400	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr19:41222400-41225600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:41222400-41225600	Active TSS	Pancreas	Pancrea
37	chr19:41222400-41226800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:41222400-41227000	Active TSS	Lung	lung
39	chr19:41222600-41224400	Active TSS	Stomach Mucosa	stomach
40	chr19:41222600-41225000	Active TSS	HSMM	muscle
41	chr19:41222600-41225400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:41222600-41225400	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr19:41222600-41225400	Active TSS	Fetal Kidney	kidney
44	chr19:41222600-41225600	Active TSS	NHDF-Ad	bronchial
45	chr19:41222600-41225800	Active TSS	NHLF	lung
46	chr19:41222600-41226200	Active TSS	HSMMtube	muscle
47	chr19:41223200-41224400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr19:41223200-41225200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr19:41223200-41225200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr19:41223200-41225600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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