Variant report

Variant	rs58051372
Chromosome Location	chr19:55850491-55850492
allele	C/G
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	RELA	chr19:55850103-55851253	GM18951	blood:	n/a	n/a
2	MAX	chr19:55849978-55851223	H1-hESC	embryonic stem cell:	n/a	chr19:55850989-55850998
3	PBX3	chr19:55850439-55851358	GM12878	blood:	n/a	chr19:55851125-55851134 chr19:55851163-55851183 chr19:55850787-55850807 chr19:55850938-55850947 chr19:55850923-55850943
4	CCNT2	chr19:55850049-55851428	K562	blood:	n/a	n/a
5	BRCA1	chr19:55850413-55850742	GM12878	blood:	n/a	chr19:55850508-55850517
6	EP300	chr19:55850041-55851033	Hela-S3	cervix:	n/a	n/a
7	BRCA1	chr19:55850253-55851230	HepG2	liver:	n/a	chr19:55850508-55850517
8	RAD21	chr19:55850280-55850929	IMR90	lung:	n/a	n/a
9	POLR2A	chr19:55850320-55853763	K562	blood:	n/a	n/a
10	JUND	chr19:55849921-55850560	T-47D	breast:	n/a	n/a
11	POLR2A	chr19:55849719-55851490	H1-hESC	embryonic stem cell:	n/a	n/a
12	HA-E2F1	chr19:55849937-55851373	MCF-7	breast:	n/a	chr19:55851332-55851341 chr19:55850655-55850667 chr19:55851053-55851062
13	JUN	chr19:55849822-55852421	K562	blood:	n/a	chr19:55850212-55850225 chr19:55850654-55850663 chr19:55851126-55851135
14	FOXP2	chr19:55850070-55851206	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr19:55850417-55850796	GM12878	blood:	n/a	n/a
16	CHD1	chr19:55850411-55851329	GM12878	blood:	n/a	n/a
17	MAX	chr19:55849880-55851712	ECC-1	luminal epithelium:	n/a	chr19:55850989-55850998 chr19:55851452-55851461
18	TFAP2C	chr19:55850004-55853125	Hela-S3	cervix:	n/a	chr19:55852681-55852696
19	TAL1	chr19:55850177-55850593	K562	blood:	n/a	n/a
20	EP300	chr19:55850134-55851226	GM12878	blood:	n/a	chr19:55851210-55851226
21	MAX	chr19:55850058-55851399	K562	blood:	n/a	chr19:55850989-55850998
22	RCOR1	chr19:55850340-55851317	GM12878	blood:	n/a	n/a
23	FOXA2	chr19:55850427-55850725	HepG2	liver:	n/a	n/a
24	ZBTB7A	chr19:55850390-55850676	K562	blood:	n/a	n/a
25	FOXA2	chr19:55849985-55851345	A549	lung:	n/a	n/a
26	PBX3	chr19:55849882-55851551	SK-N-SH	brain:	n/a	chr19:55851125-55851134 chr19:55851163-55851183 chr19:55850787-55850807 chr19:55850938-55850947 chr19:55850923-55850943
27	MXI1	chr19:55849731-55853168	SK-N-SH	brain:	n/a	chr19:55850630-55850645 chr19:55850628-55850643
28	REST	chr19:55849678-55852977	H1-neurons	neurons:	n/a	chr19:55850854-55850867 chr19:55852837-55852857 chr19:55852394-55852407 chr19:55852837-55852857 chr19:55850816-55850825 chr19:55852837-55852857 chr19:55852179-55852192 chr19:55852840-55852853
29	KAP1	chr19:55849971-55850677	K562	blood:	n/a	n/a
30	CREB1	chr19:55849965-55851771	K562	blood:	n/a	n/a
31	SP1	chr19:55850383-55851361	GM12878	blood:	n/a	chr19:55850702-55850715 chr19:55851059-55851069 chr19:55851123-55851144 chr19:55850654-55850665 chr19:55850566-55850580 chr19:55851058-55851070 chr19:55851058-55851070 chr19:55851176-55851197 chr19:55851059-55851069
32	STAT5A	chr19:55850019-55850576	GM12878	blood:	n/a	n/a
33	RFX5	chr19:55849820-55851612	SK-N-SH	brain:	n/a	chr19:55850988-55851003 chr19:55850628-55850645 chr19:55850629-55850644 chr19:55850938-55850947 chr19:55850629-55850644 chr19:55851146-55851160 chr19:55850629-55850644
34	POLR2A	chr19:55850462-55850733	A549	lung:	n/a	n/a
35	CEBPB	chr19:55849868-55851369	A549	lung:	n/a	n/a
36	MAX	chr19:55850033-55851413	HepG2	liver:	n/a	chr19:55850989-55850998
37	GATA3	chr19:55849697-55851574	A549	lung:	n/a	n/a
38	POLR2A	chr19:55850443-55851728	MCF-7	breast:	n/a	n/a
39	FOS	chr19:55850067-55851329	Hela-S3	cervix:	n/a	chr19:55850654-55850663 chr19:55851126-55851135
40	MYC	chr19:55849999-55851718	K562	blood:	n/a	chr19:55850989-55850998 chr19:55851452-55851461
41	TCF12	chr19:55849973-55850530	A549	lung:	n/a	n/a
42	GATA3	chr19:55849844-55851424	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr19:55850476-55851938	GM12878	blood:	n/a	n/a
44	RELA	chr19:55850136-55851259	GM15510	blood:	n/a	n/a
45	GATA3	chr19:55850053-55850524	SH-SY5Y	brain:	n/a	n/a
46	REST	chr19:55849774-55851479	H1-neurons	neurons:	n/a	chr19:55850854-55850867 chr19:55850816-55850825
47	ATF2	chr19:55849903-55850766	H1-hESC	embryonic stem cell:	n/a	n/a
48	TBP	chr19:55850056-55851365	HepG2	liver:	n/a	n/a
49	EP300	chr19:55849938-55851383	A549	lung:	n/a	chr19:55851210-55851226
50	RCOR1	chr19:55849982-55851805	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55834572..55838662-chr19:55847214..55851799,6	K562	blood:
2	chr19:55812251..55815650-chr19:55848570..55851424,4	MCF-7	breast:
3	chr19:55850053..55852875-chr19:55917610..55920825,5	MCF-7	breast:
4	chr19:55770686..55772282-chr19:55848676..55850979,2	K562	blood:
5	chr19:55848515..55857343-chr19:55894079..55900232,19	MCF-7	breast:
6	chr19:55848855..55851022-chr19:55968607..55971004,2	MCF-7	breast:
7	chr19:55788649..55794261-chr19:55847636..55852828,10	K562	blood:
8	chr19:55834572..55838022-chr19:55847724..55851799,4	K562	blood:
9	chr19:55850159..55852267-chr19:56116484..56118952,2	MCF-7	breast:
10	chr19:55847527..55853936-chr19:55895162..55898950,13	K562	blood:
11	chr19:55849062..55852611-chr19:55879307..55883496,5	MCF-7	breast:
12	chr19:55790045..55791863-chr19:55848758..55853021,3	MCF-7	breast:
13	chr19:55789812..55792675-chr19:55848548..55852419,5	K562	blood:
14	chr19:55849530..55854944-chr19:55915448..55920939,7	K562	blood:
15	chr19:55849599..55852921-chr19:55970880..55974521,5	K562	blood:
16	chr19:55815976..55818452-chr19:55849117..55850810,2	MCF-7	breast:
17	chr19:55848915..55854876-chr19:55892600..55899757,13	MCF-7	breast:
18	chr19:55847613..55856135-chr19:55893756..55900268,15	K562	blood:
19	chr11:62608651..62609630-chr19:55850203..55850703,2	Hela-S3	cervix:

Variant related genes	Relation type
SUV420H2	TF binding region
ENSG00000267531	TF binding region
ENSG00000108107	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000180061	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000095752	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000261221	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10416740	0.98[EUR][1000 genomes]
rs11879143	0.98[EUR][1000 genomes]
rs12609926	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59262883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59493644	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59695872	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59944279	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73605199	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73605200	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73605202	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73607003	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73607005	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73607008	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73607019	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73607024	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
7	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv912461	chr19:55845386-55897327	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
9	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
11	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
12	esv1796007	chr19:55850269-55851289	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
13	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55849600-55850600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:55849600-55850600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:55849600-55850600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:55849800-55850600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:55849800-55850600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:55849800-55850600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:55849800-55850600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr19:55849800-55850600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr19:55849800-55850600	Flanking Active TSS	Fetal Lung	lung
10	chr19:55849800-55850600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr19:55849800-55850600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr19:55849800-55850600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr19:55849800-55850600	Flanking Active TSS	Dnd41	blood
14	chr19:55849800-55850600	Flanking Active TSS	Hela-S3	cervix
15	chr19:55849800-55850600	Flanking Bivalent TSS/Enh	HepG2	liver
16	chr19:55849800-55850600	Flanking Active TSS	HMEC	breast
17	chr19:55849800-55851600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:55849800-55851600	Active TSS	Fetal Brain Female	brain
19	chr19:55849800-55851800	Active TSS	Brain Germinal Matrix	brain
20	chr19:55849800-55851800	Active TSS	Brain Hippocampus Middle	brain
21	chr19:55849800-55852800	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:55849800-55852800	Active TSS	A549	lung
23	chr19:55849800-55853000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr19:55850000-55850600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr19:55850000-55850600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:55850000-55850600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:55850000-55850600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:55850000-55850600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr19:55850000-55850600	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr19:55850000-55850600	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr19:55850000-55850600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr19:55850000-55850600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr19:55850000-55850600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr19:55850000-55850600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr19:55850000-55850600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr19:55850000-55850600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:55850000-55850600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr19:55850000-55850600	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr19:55850000-55850600	Flanking Active TSS	Colonic Mucosa	Colon
40	chr19:55850000-55850600	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr19:55850000-55850600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr19:55850000-55850600	Flanking Active TSS	Fetal Brain Male	brain
43	chr19:55850000-55850600	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr19:55850000-55850600	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr19:55850000-55850600	Flanking Active TSS	Fetal Thymus	thymus
46	chr19:55850000-55850600	Flanking Active TSS	Pancreas	Pancrea
47	chr19:55850000-55850600	Active TSS	Placenta Amnion	Placenta Amnion
48	chr19:55850000-55850600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:55850000-55850600	Flanking Active TSS	Right Ventricle	heart
50	chr19:55850000-55850600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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