Variant report

Variant	rs59695872
Chromosome Location	chr19:55851989-55851990
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	POLR2A	chr19:55850320-55853763	K562	blood:	n/a	n/a
2	UBTF	chr19:55851022-55852863	K562	blood:	n/a	n/a
3	JUN	chr19:55849822-55852421	K562	blood:	n/a	chr19:55850212-55850225 chr19:55850654-55850663 chr19:55851126-55851135
4	TFAP2C	chr19:55850004-55853125	Hela-S3	cervix:	n/a	chr19:55852681-55852696
5	CTCF	chr19:55851840-55851990	GM12874	blood:	n/a	n/a
6	MXI1	chr19:55849731-55853168	SK-N-SH	brain:	n/a	chr19:55850630-55850645 chr19:55850628-55850643
7	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
8	POLR2A	chr19:55850718-55852051	HCT-116	colon:	n/a	n/a
9	YY1	chr19:55851939-55852086	K562	blood:	n/a	n/a
10	ZBTB7A	chr19:55850990-55852824	K562	blood:	n/a	chr19:55852298-55852307 chr19:55852172-55852181
11	SMARCB1	chr19:55849985-55852698	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:55849997-55853223	SK-N-MC	brain:	n/a	n/a
13	NR2F2	chr19:55851406-55852040	K562	blood:	n/a	n/a
14	POLR2A	chr19:55851895-55852101	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr19:55851880-55852030	GM12865	blood:	n/a	n/a
16	POLR2A	chr19:55849954-55852022	PBDE	blood:	n/a	n/a
17	POLR2A	chr19:55851937-55852872	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr19:55850361-55853075	PFSK-1	brain:	n/a	n/a
19	ZBTB7A	chr19:55851388-55852638	ECC-1	luminal epithelium:	n/a	chr19:55852298-55852307 chr19:55852172-55852181
20	TFAP2A	chr19:55850046-55853057	Hela-S3	cervix:	n/a	chr19:55852683-55852693 chr19:55852683-55852693 chr19:55851680-55851695 chr19:55850418-55850429 chr19:55852174-55852185 chr19:55852683-55852693 chr19:55850418-55850429 chr19:55852683-55852693 chr19:55850418-55850429 chr19:55850418-55850429 chr19:55852173-55852185
21	CTCF	chr19:55851980-55852130	HCFaa	heart:	n/a	n/a
22	POLR2A	chr19:55849959-55853034	K562	blood:	n/a	n/a
23	POLR2A	chr19:55850420-55852188	K562	blood:	n/a	n/a
24	NR2F2	chr19:55851388-55852116	K562	blood:	n/a	n/a
25	POLR2A	chr19:55851980-55852930	H1-neurons	neurons:	n/a	n/a
26	HMGN3	chr19:55850513-55852473	K562	blood:	n/a	n/a
27	POLR2A	chr19:55850432-55853023	K562	blood:	n/a	n/a
28	HEY1	chr19:55851406-55852514	K562	blood:	n/a	n/a
29	ZNF263	chr19:55851889-55852488	HEK293-T-REx	kidney:	n/a	chr19:55852117-55852138 chr19:55852095-55852104
30	POLR2A	chr19:55849951-55852760	K562	blood:	n/a	n/a
31	STAT5A	chr19:55851711-55852212	GM12878	blood:	n/a	chr19:55851814-55851826
32	POLR2A	chr19:55850043-55852357	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr19:55849929-55853529	K562	blood:	n/a	n/a
34	NR2F2	chr19:55850975-55852080	MCF-7	breast:	n/a	n/a
35	MAZ	chr19:55849974-55853079	IMR90	lung:	n/a	chr19:55852733-55852743 chr19:55850989-55850998 chr19:55851452-55851461
36	MAX	chr19:55851976-55853353	K562	blood:	n/a	chr19:55852733-55852743
37	POLR2A	chr19:55851015-55852768	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr19:55851867-55852228	ECC-1	luminal epithelium:	n/a	n/a
39	CHD2	chr19:55850008-55852138	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr19:55851406-55852470	A549	lung:	n/a	n/a
41	ZBTB7A	chr19:55851529-55852489	K562	blood:	n/a	chr19:55852298-55852307 chr19:55852172-55852181
42	POLR2A	chr19:55850533-55852478	HepG2	liver:	n/a	n/a
43	POLR2A	chr19:55851082-55852080	IMR90	lung:	n/a	n/a
44	CTCF	chr19:55851840-55851990	GM12873	blood:	n/a	n/a
45	CTCF	chr19:55851840-55851990	GM12871	blood:	n/a	n/a
46	SIN3A	chr19:55851574-55852547	H1-hESC	embryonic stem cell:	n/a	chr19:55852060-55852073 chr19:55852273-55852286
47	POLR2A	chr19:55849827-55852240	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr19:55849896-55852297	Hela-S3	cervix:	n/a	n/a
49	TCF12	chr19:55851419-55853180	A549	lung:	n/a	chr19:55852609-55852617 chr19:55852265-55852275
50	POLR2A	chr19:55851783-55852152	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55851487..55853796-chr19:55888849..55891400,2	MCF-7	breast:
2	chr19:55769739..55771684-chr19:55850814..55852866,2	MCF-7	breast:
3	chr19:55850053..55852875-chr19:55917610..55920825,5	MCF-7	breast:
4	chr19:55720239..55723202-chr19:55851102..55853910,2	MCF-7	breast:
5	chr19:55848515..55857343-chr19:55894079..55900232,19	MCF-7	breast:
6	chr19:55813078..55815879-chr19:55851167..55852905,2	K562	blood:
7	chr19:55788649..55794261-chr19:55847636..55852828,10	K562	blood:
8	chr19:55850159..55852267-chr19:56116484..56118952,2	MCF-7	breast:
9	chr19:55847527..55853936-chr19:55895162..55898950,13	K562	blood:
10	chr19:55849062..55852611-chr19:55879307..55883496,5	MCF-7	breast:
11	chr19:55814784..55816804-chr19:55850965..55853492,2	K562	blood:
12	chr19:55790045..55791863-chr19:55848758..55853021,3	MCF-7	breast:
13	chr19:55813052..55817410-chr19:55850511..55853343,6	MCF-7	breast:
14	chr19:55789812..55792675-chr19:55848548..55852419,5	K562	blood:
15	chr19:55849530..55854944-chr19:55915448..55920939,7	K562	blood:
16	chr19:55851377..55854272-chr19:55873809..55875979,2	MCF-7	breast:
17	chr19:55851056..55852786-chr19:55880756..55882333,2	MCF-7	breast:
18	chr19:55849599..55852921-chr19:55970880..55974521,5	K562	blood:
19	chr19:55848915..55854876-chr19:55892600..55899757,13	MCF-7	breast:
20	chr19:55847613..55856135-chr19:55893756..55900268,15	K562	blood:

Variant related genes	Relation type
SUV420H2	TF binding region
ENSG00000063241	Chromatin interaction
ENSG00000095752	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000180043	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000269275	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000108106	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	0.96[EUR][1000 genomes]
rs11879143	0.96[EUR][1000 genomes]
rs12609926	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58051372	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59262883	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59493644	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59944279	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73605199	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73605200	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73605202	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73607003	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73607005	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73607008	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73607019	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73607024	0.91[AMR][1000 genomes];0.96[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	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
13	esv1799638	chr19:55850652-55883879	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 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	chr19:55849800-55852800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:55849800-55852800	Active TSS	A549	lung
3	chr19:55849800-55853000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr19:55850000-55852000	Active TSS	Thymus	Thymus
5	chr19:55850000-55852200	Active TSS	Left Ventricle	heart
6	chr19:55850000-55852400	Active TSS	Aorta	Aorta
7	chr19:55850000-55852800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:55850000-55852800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:55850000-55852800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:55850000-55853200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr19:55850200-55852000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:55850200-55852000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:55850200-55852800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr19:55850200-55852800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:55850200-55852800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr19:55850200-55852800	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr19:55850200-55852800	Active TSS	Fetal Kidney	kidney
18	chr19:55850200-55852800	Active TSS	Ovary	ovary
19	chr19:55850400-55852000	Active TSS	Brain Cingulate Gyrus	brain
20	chr19:55850400-55852000	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr19:55850400-55852800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:55850400-55852800	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr19:55850400-55852800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:55850400-55852800	Active TSS	Colon Smooth Muscle	Colon
25	chr19:55850400-55852800	Active TSS	K562	blood
26	chr19:55850400-55853000	Active TSS	Brain Anterior Caudate	brain
27	chr19:55850600-55852000	Active TSS	Dnd41	blood
28	chr19:55850600-55852000	Bivalent/Poised TSS	HepG2	liver
29	chr19:55850600-55852400	Active TSS	Fetal Lung	lung
30	chr19:55850600-55852800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:55850600-55852800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr19:55850600-55852800	Active TSS	Fetal Intestine Small	intestine
33	chr19:55850600-55852800	Active TSS	GM12878-XiMat	blood
34	chr19:55850600-55852800	Active TSS	HSMM	muscle
35	chr19:55851200-55852000	Active TSS	Right Atrium	heart
36	chr19:55851200-55852000	Active TSS	Small Intestine	intestine
37	chr19:55851200-55852200	Active TSS	Lung	lung
38	chr19:55851200-55852800	Active TSS	HSMMtube	muscle
39	chr19:55851400-55852000	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr19:55851400-55852400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:55851400-55852400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:55851400-55852600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr19:55851400-55852600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:55851400-55852600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr19:55851400-55852600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:55851400-55852600	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr19:55851400-55852600	Flanking Active TSS	Placenta	Placenta
48	chr19:55851400-55852600	Active TSS	NHDF-Ad	bronchial
49	chr19:55851400-55852800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr19:55851400-55852800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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