Variant report

Variant	rs2561531
Chromosome Location	chr19:41221919-41221920
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	JUND	chr19:41220722-41223493	A549	lung:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222080-41222091 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
3	FOSL2	chr19:41221341-41222432	MCF-7	breast:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
4	POLR2A	chr19:41220704-41223405	Raji	blood:	n/a	n/a
5	SP1	chr19:41220495-41223600	A549	lung:	n/a	chr19:41222709-41222723 chr19:41220745-41220759 chr19:41222798-41222807 chr19:41222861-41222870 chr19:41221025-41221034 chr19:41222705-41222716 chr19:41222861-41222870 chr19:41222860-41222870 chr19:41221456-41221470 chr19:41222599-41222611 chr19:41222860-41222869 chr19:41222859-41222871 chr19:41221602-41221611 chr19:41222599-41222611 chr19:41222796-41222808 chr19:41221879-41221893 chr19:41222859-41222871 chr19:41222919-41222928 chr19:41221600-41221612 chr19:41222969-41222979 chr19:41222600-41222609 chr19:41222969-41222979
6	BCL3	chr19:41220248-41225401	A549	lung:	n/a	chr19:41225228-41225237 chr19:41222875-41222884 chr19:41222082-41222091 chr19:41222234-41222243
7	TEAD4	chr19:41221397-41221939	ECC-1	luminal epithelium:	n/a	n/a
8	JUND	chr19:41221491-41223085	K562	blood:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222080-41222091 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
9	NR3C1	chr19:41221279-41222407	A549	lung:	n/a	chr19:41221814-41221823 chr19:41221815-41221824 chr19:41221588-41221597 chr19:41221693-41221702 chr19:41221664-41221682 chr19:41221584-41221597
10	GATA3	chr19:41221383-41223122	MCF-7	breast:	n/a	chr19:41222790-41222798
11	IRF3	chr19:41220953-41221969	Hela-S3	cervix:	n/a	chr19:41221598-41221612
12	TCF12	chr19:41220427-41223301	SK-N-SH	brain:	n/a	chr19:41221137-41221145
13	RUNX3	chr19:41221350-41223167	GM12878	blood:	n/a	n/a
14	MAFK	chr19:41221370-41222810	IMR90	lung:	n/a	chr19:41221687-41221702 chr19:41222180-41222190 chr19:41221692-41221701 chr19:41221692-41221702 chr19:41221456-41221471 chr19:41221691-41221705 chr19:41221690-41221706
15	ZNF263	chr19:41221275-41223163	HEK293-T-REx	kidney:	n/a	chr19:41221462-41221471
16	SP1	chr19:41220643-41223291	HCT-116	colon:	n/a	chr19:41222709-41222723 chr19:41220745-41220759 chr19:41222798-41222807 chr19:41222861-41222870 chr19:41221025-41221034 chr19:41222705-41222716 chr19:41222861-41222870 chr19:41222860-41222870 chr19:41221456-41221470 chr19:41222599-41222611 chr19:41222860-41222869 chr19:41222859-41222871 chr19:41221602-41221611 chr19:41222599-41222611 chr19:41222796-41222808 chr19:41221879-41221893 chr19:41222859-41222871 chr19:41222919-41222928 chr19:41221600-41221612 chr19:41222969-41222979 chr19:41222600-41222609 chr19:41222969-41222979
17	MAX	chr19:41221159-41222903	MCF-7	breast:	n/a	chr19:41222713-41222723 chr19:41222082-41222091
18	POLR2A	chr19:41221313-41223239	Hela-S3	cervix:	n/a	n/a
19	E2F6	chr19:41221743-41221994	K562	blood:	n/a	n/a
20	STAT3	chr19:41221267-41222409	MCF10A-Er-Src	breast:	n/a	chr19:41222081-41222090 chr19:41221661-41221669 chr19:41222150-41222162 chr19:41221879-41221891 chr19:41221659-41221670
21	CHD2	chr19:41220733-41221996	GM12878	blood:	n/a	chr19:41220935-41220945
22	POLR2A	chr19:41220316-41225389	H1-hESC	embryonic stem cell:	n/a	n/a
23	TBP	chr19:41221130-41223029	GM12878	blood:	n/a	n/a
24	USF1	chr19:41221396-41222288	A549	lung:	n/a	n/a
25	MAFK	chr19:41221473-41222321	K562	blood:	n/a	chr19:41221687-41221702 chr19:41222180-41222190 chr19:41221692-41221701 chr19:41221692-41221702 chr19:41221691-41221705 chr19:41221690-41221706
26	GATA3	chr19:41221335-41222975	MCF-7	breast:	n/a	chr19:41222790-41222798
27	JUND	chr19:41221436-41222946	MCF-7	breast:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222080-41222091 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
28	CEBPB	chr19:41220757-41223142	A549	lung:	n/a	n/a
29	SIX5	chr19:41221000-41222979	A549	lung:	n/a	n/a
30	POLR2A	chr19:41221790-41223141	GM12878	blood:	n/a	n/a
31	SIN3AK20	chr19:41220913-41223137	A549	lung:	n/a	n/a
32	POLR2A	chr19:41221274-41223569	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:41221467-41223425	GM12878	blood:	n/a	n/a
34	CUX1	chr19:41221560-41222332	GM12878	blood:	n/a	n/a
35	CREB1	chr19:41221328-41221950	A549	lung:	n/a	n/a
36	TEAD4	chr19:41221309-41222508	SK-N-SH	brain:	n/a	n/a
37	GABPA	chr19:41221370-41223230	MCF-7	breast:	n/a	chr19:41221602-41221611
38	JUN	chr19:41221560-41222284	K562	blood:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
39	SMARCC1	chr19:41220859-41223014	Hela-S3	cervix:	n/a	chr19:41221815-41221824 chr19:41222081-41222090
40	POLR2A	chr19:41221306-41223428	HCT-116	colon:	n/a	n/a
41	GTF3C2	chr19:41221599-41223158	K562	blood:	n/a	n/a
42	BACH1	chr19:41221515-41222062	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:41220655-41223480	GM12878	blood:	n/a	n/a
44	FOSL2	chr19:41221364-41222398	SK-N-SH	brain:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222081-41222091 chr19:41221813-41221825 chr19:41222081-41222091 chr19:41222081-41222091 chr19:41221815-41221823 chr19:41222179-41222189 chr19:41222081-41222091 chr19:41222081-41222090
45	ZKSCAN1	chr19:41221005-41223240	Hela-S3	cervix:	n/a	n/a
46	SIN3A	chr19:41220570-41224559	H1-hESC	embryonic stem cell:	n/a	chr19:41222914-41222925
47	REST	chr19:41220437-41223042	A549	lung:	n/a	chr19:41222176-41222196 chr19:41221597-41221607
48	MAZ	chr19:41220727-41223303	K562	blood:	n/a	chr19:41222713-41222723 chr19:41222082-41222091
49	TEAD4	chr19:41220774-41222056	A549	lung:	n/a	n/a
50	JUND	chr19:41221535-41223328	H1-hESC	embryonic stem cell:	n/a	chr19:41221814-41221824 chr19:41222178-41222189 chr19:41222080-41222091 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

No.	Distal block	Cell Line	Cell type
1	chr19:41219466..41223288-chr19:41281896..41285456,5	MCF-7	breast:
2	chr19:41110008..41112738-chr19:41221401..41222982,2	MCF-7	breast:
3	chr19:41220672..41223321-chr19:41282772..41284711,3	K562	blood:
4	chr19:41221300..41223743-chr19:41303378..41306610,3	MCF-7	breast:
5	chr19:41113914..41116044-chr19:41221538..41224427,3	MCF-7	breast:
6	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
7	chr19:41220938..41225137-chr19:41311275..41314518,5	K562	blood:
8	chr14:73525186..73525709-chr19:41221567..41222516,2	Hela-S3	cervix:
9	chr19:40949347..40951622-chr19:41220868..41223140,2	MCF-7	breast:
10	chr19:41221165..41222932-chr19:41261508..41263224,2	MCF-7	breast:
11	chr19:41220005..41225073-chr19:41230462..41235365,8	K562	blood:
12	chr19:41220377..41222544-chr19:41768201..41769798,2	MCF-7	breast:
13	chr19:41193561..41199772-chr19:41221208..41225709,11	K562	blood:
14	chr19:41221538..41223321-chr19:41282786..41284711,2	K562	blood:
15	chr19:41213611..41215968-chr19:41219093..41222083,3	MCF-7	breast:
16	chr19:41207302..41211180-chr19:41220761..41224340,7	K562	blood:
17	chr19:41221472..41222399-chr7:92219229..92219756,2	Hela-S3	cervix:
18	chr19:41194805..41199772-chr19:41221674..41225965,11	K562	blood:
19	chr19:41219701..41226727-chr19:41253156..41258804,17	K562	blood:
20	chr19:41219692..41221966-chr19:41769353..41771568,2	MCF-7	breast:
21	chr19:41205738..41209357-chr19:41220858..41225801,5	MCF-7	breast:
22	chr19:41188510..41190194-chr19:41220428..41221993,2	K562	blood:
23	chr19:41220807..41223667-chr19:41282098..41285361,4	MCF-7	breast:
24	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:
25	chr19:40949565..40951989-chr19:41219354..41222014,2	K562	blood:
26	chr19:41187452..41189406-chr19:41221376..41223661,2	MCF-7	breast:
27	chr19:41220057..41225402-chr19:41302090..41307926,9	MCF-7	breast:
28	chr19:40971240..40973961-chr19:41221836..41225167,3	MCF-7	breast:
29	chr19:41220988..41222886-chr19:41267608..41270115,2	MCF-7	breast:
30	chr19:41221453..41223468-chr19:41246365..41247883,2	MCF-7	breast:
31	chr19:41220238..41223312-chr19:41303618..41307521,4	K562	blood:
32	chr19:41221436..41223725-chr19:41310201..41314445,5	MCF-7	breast:
33	chr19:41219701..41225554-chr19:41255271..41259667,13	K562	blood:
34	chr19:40948713..40950768-chr19:41219384..41222098,2	K562	blood:
35	chr19:41219625..41226874-chr19:41252287..41258959,29	MCF-7	breast:
36	chr19:41220720..41224635-chr19:41312175..41316788,5	MCF-7	breast:
37	chr19:41193720..41198590-chr19:41218677..41224410,19	MCF-7	breast:
38	chr19:41219350..41226574-chr19:41253922..41258567,22	MCF-7	breast:
39	chr19:41220581..41222873-chr19:41307320..41309933,2	MCF-7	breast:
40	chr19:41221142..41224353-chr19:41311383..41314668,3	K562	blood:

Variant related genes	Relation type
ITPKC	TF binding region
ADCK4	TF binding region
ENSG00000086544	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000268797	Chromatin interaction
ENSG00000234545	Chromatin interaction
ENSG00000105245	Chromatin interaction
ENSG00000119707	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000160460	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000223284	Chromatin interaction
ENSG00000090013	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10420651	0.92[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs10420685	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs13108	0.85[CHB][hapmap]
rs1455434	1.00[CHB][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs1531063	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17726258	0.92[CHB][hapmap];0.85[GIH][hapmap]
rs1869710	1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs2233154	0.85[CHB][hapmap]
rs2233156	0.92[CHB][hapmap];0.85[GIH][hapmap]
rs2233159	0.85[CHB][hapmap]
rs2249854	0.85[CHB][hapmap]
rs2254326	0.92[CHB][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2254338	0.83[EUR][1000 genomes]
rs2303723	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2545763	0.85[GIH][hapmap]
rs2545771	0.85[GIH][hapmap]
rs2561529	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2604866	0.85[GIH][hapmap]
rs2607416	0.92[CHB][hapmap]
rs2607418	0.92[CHB][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2607425	0.85[CHB][hapmap]
rs2607426	0.85[CHB][hapmap]
rs34633896	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3745212	0.89[EUR][1000 genomes]
rs7250888	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107978	0.85[CHB][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41219800-41222600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:41219800-41222800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:41220000-41222600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:41220200-41222000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr19:41220200-41222600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr19:41220200-41222600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr19:41220200-41222600	Flanking Active TSS	Fetal Muscle Trunk	muscle
8	chr19:41220200-41222600	Flanking Active TSS	Fetal Muscle Leg	muscle
9	chr19:41220200-41222600	Flanking Active TSS	Dnd41	blood
10	chr19:41220200-41222600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr19:41220200-41222800	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr19:41220400-41222000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:41220400-41222400	Flanking Active TSS	K562	blood
14	chr19:41220400-41222600	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr19:41220400-41222600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:41220400-41222600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr19:41220400-41222600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr19:41220400-41222600	Flanking Active TSS	Liver	Liver
19	chr19:41220400-41222600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr19:41220400-41222600	Flanking Active TSS	HUVEC	blood vessel
21	chr19:41220400-41222800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
22	chr19:41220400-41222800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr19:41220400-41225400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:41220400-41225600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr19:41220400-41225800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr19:41220400-41226800	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr19:41220600-41222000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:41220600-41224800	Active TSS	Right Ventricle	heart
29	chr19:41220600-41225200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:41220600-41225400	Active TSS	Left Ventricle	heart
31	chr19:41220600-41225400	Active TSS	Psoas Muscle	Psoas
32	chr19:41220600-41225600	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:41220600-41225600	Active TSS	Aorta	Aorta
34	chr19:41220600-41225800	Active TSS	Gastric	stomach
35	chr19:41220600-41226400	Active TSS	Right Atrium	heart
36	chr19:41220600-41227000	Active TSS	Esophagus	oesophagus
37	chr19:41220800-41226200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:41221000-41222000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:41221000-41222600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr19:41221000-41225200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr19:41221200-41222400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:41221200-41222400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:41221200-41222400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr19:41221200-41222400	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr19:41221200-41222400	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr19:41221200-41222400	Flanking Active TSS	Fetal Brain Female	brain
47	chr19:41221200-41222400	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr19:41221200-41222400	Flanking Active TSS	Fetal Lung	lung
49	chr19:41221200-41222400	Flanking Active TSS	A549	lung
50	chr19:41221200-41222400	Flanking Active TSS	Hela-S3	cervix

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