Variant report

Variant	rs59224814
Chromosome Location	chr19:55690120-55690121
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	HCFC1	chr19:55690088-55690969	K562	blood:	n/a	n/a
2	JUND	chr19:55690090-55690906	A549	lung:	n/a	chr19:55690279-55690293
3	YY1	chr19:55690061-55690744	GM12878	blood:	n/a	n/a
4	SP1	chr19:55689984-55690977	GM12878	blood:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690845-55690854 chr19:55690307-55690317 chr19:55690843-55690855 chr19:55690701-55690714
5	JUN	chr19:55689997-55692239	K562	blood:	n/a	chr19:55690959-55690968 chr19:55690279-55690293
6	CREB1	chr19:55690031-55691002	H1-hESC	embryonic stem cell:	n/a	n/a
7	SP1	chr19:55689974-55690973	GM12878	blood:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690845-55690854 chr19:55690307-55690317 chr19:55690843-55690855 chr19:55690701-55690714
8	REST	chr19:55690103-55690401	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr19:55690046-55690431	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr19:55690062-55690607	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:55690065-55692089	H1-neurons	neurons:	n/a	n/a
12	MAZ	chr19:55690105-55691151	HepG2	liver:	n/a	n/a
13	REST	chr19:55690082-55692299	A549	lung:	n/a	chr19:55691568-55691588 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
14	SIN3A	chr19:55690044-55691845	H1-hESC	embryonic stem cell:	n/a	chr19:55691573-55691587 chr19:55691577-55691586 chr19:55691568-55691581 chr19:55691592-55691605
15	ZNF384	chr19:55689924-55690403	K562	blood:	n/a	n/a
16	REST	chr19:55689830-55692121	H1-neurons	neurons:	n/a	chr19:55691568-55691588 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
17	JUND	chr19:55690103-55690399	HepG2	liver:	n/a	chr19:55690279-55690293
18	TEAD4	chr19:55689974-55690425	HepG2	liver:	n/a	n/a
19	CHD2	chr19:55689989-55690890	H1-hESC	embryonic stem cell:	n/a	chr19:55690694-55690704
20	SIX5	chr19:55689962-55691205	A549	lung:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
21	RCOR1	chr19:55690080-55690355	K562	blood:	n/a	n/a
22	SP1	chr19:55689929-55691037	A549	lung:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690845-55690854 chr19:55690307-55690317 chr19:55690843-55690855 chr19:55690701-55690714
23	SIX5	chr19:55690089-55690882	H1-hESC	embryonic stem cell:	n/a	chr19:55690579-55690588 chr19:55690577-55690586 chr19:55690638-55690654
24	JUND	chr19:55690103-55690819	K562	blood:	n/a	chr19:55690279-55690293
25	GABPA	chr19:55690105-55690993	K562	blood:	n/a	n/a
26	GTF2F1	chr19:55690110-55690434	H1-hESC	embryonic stem cell:	n/a	n/a
27	SIN3AK20	chr19:55690075-55691046	H1-hESC	embryonic stem cell:	n/a	n/a
28	YY1	chr19:55690102-55690324	GM12891	blood:	n/a	n/a
29	CUX1	chr19:55690017-55690196	GM12878	blood:	n/a	n/a
30	REST	chr19:55690108-55692190	A549	lung:	n/a	chr19:55691568-55691588 chr19:55691592-55691605 chr19:55691568-55691588 chr19:55691574-55691588 chr19:55691568-55691581 chr19:55691576-55691586 chr19:55691571-55691584 chr19:55691455-55691468 chr19:55691568-55691588 chr19:55691571-55691584 chr19:55691569-55691587 chr19:55691568-55691577
31	YY1	chr19:55690004-55690591	H1-hESC	embryonic stem cell:	n/a	n/a
32	SP1	chr19:55689896-55690572	H1-hESC	embryonic stem cell:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690307-55690317
33	MAFK	chr19:55690096-55690779	H1-hESC	embryonic stem cell:	n/a	n/a
34	SREBP1	chr19:55689965-55691217	GM12878	blood:	n/a	chr19:55690813-55690827 chr19:55690831-55690845 chr19:55690832-55690846 chr19:55690812-55690826
35	MXI1	chr19:55689999-55692497	IMR90	lung:	n/a	chr19:55690830-55690845 chr19:55690811-55690826 chr19:55690832-55690847 chr19:55690813-55690828
36	TEAD4	chr19:55689995-55690407	K562	blood:	n/a	n/a
37	RAD21	chr19:55690075-55690455	SK-N-SH_RA	brain:	n/a	n/a
38	ZNF384	chr19:55689996-55690249	GM12878	blood:	n/a	n/a
39	GATA3	chr19:55689889-55690214	SH-SY5Y	brain:	n/a	n/a
40	SP1	chr19:55689974-55690675	HepG2	liver:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690307-55690317
41	ELF1	chr19:55690112-55690900	A549	lung:	n/a	chr19:55690718-55690727
42	MAX	chr19:55690071-55692000	A549	lung:	n/a	chr19:55691737-55691747 chr19:55691555-55691562 chr19:55691556-55691565 chr19:55691458-55691468 chr19:55691554-55691564
43	SP4	chr19:55689899-55690761	H1-hESC	embryonic stem cell:	n/a	n/a
44	ETS1	chr19:55689979-55690921	A549	lung:	n/a	chr19:55690719-55690728 chr19:55690719-55690728 chr19:55690720-55690730 chr19:55690576-55690589 chr19:55690578-55690585 chr19:55690719-55690730 chr19:55690507-55690520 chr19:55690719-55690728 chr19:55690717-55690726 chr19:55690719-55690728 chr19:55690718-55690727 chr19:55690716-55690729 chr19:55690719-55690728 chr19:55690719-55690728 chr19:55690506-55690519
45	SP1	chr19:55689734-55691025	HCT-116	colon:	n/a	chr19:55690308-55690317 chr19:55690262-55690274 chr19:55690845-55690854 chr19:55690307-55690317 chr19:55690843-55690855 chr19:55690701-55690714
46	ZNF143	chr19:55690071-55691013	H1-hESC	embryonic stem cell:	n/a	chr19:55690508-55690526 chr19:55690577-55690586 chr19:55690655-55690673 chr19:55690570-55690588 chr19:55690512-55690531 chr19:55690579-55690588 chr19:55690410-55690428
47	JUND	chr19:55690092-55690460	H1-hESC	embryonic stem cell:	n/a	chr19:55690279-55690293
48	JUND	chr19:55690029-55690930	H1-hESC	embryonic stem cell:	n/a	chr19:55690279-55690293
49	ZBTB7A	chr19:55690110-55690396	K562	blood:	n/a	n/a
50	MXI1	chr19:55689809-55692060	SK-N-SH	brain:	n/a	chr19:55690830-55690845 chr19:55690811-55690826 chr19:55690832-55690847 chr19:55690813-55690828

No.	Distal block	Cell Line	Cell type
1	chr19:55516495..55518136-chr19:55689009..55691049,2	K562	blood:
2	chr19:55687947..55690269-chr19:55790168..55793036,2	MCF-7	breast:
3	chr19:55688311..55691062-chr19:55894842..55896433,2	MCF-7	breast:
4	chr19:55688939..55693251-chr19:55917287..55920595,8	K562	blood:
5	chr19:55689704..55692023-chr19:55769514..55771598,2	K562	blood:
6	chr19:55690071..55692651-chr19:55739628..55742521,2	MCF-7	breast:
7	chr19:55688567..55692973-chr19:55725028..55730023,9	K562	blood:
8	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
9	chr19:55687645..55690353-chr19:55769334..55772145,4	K562	blood:
10	chr19:55689066..55691659-chr19:55726623..55728296,2	MCF-7	breast:
11	chr19:55688770..55691626-chr19:55917418..55920191,3	K562	blood:
12	chr19:55690042..55692776-chr19:55717237..55718780,2	K562	blood:
13	chr19:55688544..55691824-chr19:55726439..55729589,6	K562	blood:
14	chr19:55626440..55629266-chr19:55687388..55690294,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55689300-55690562	l_1714_chr19:55688749-55693967_brain

Variant related genes	Relation type
SYT5	TF binding region
ENSG00000105063	Chromatin interaction
ENSG00000267265	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000080031	Chromatin interaction
ENSG00000180089	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000133265	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11666987	0.83[ASN][1000 genomes]
rs2288525	0.83[ASN][1000 genomes]
rs2288526	0.83[ASN][1000 genomes]
rs2288527	0.83[ASN][1000 genomes]
rs3760867	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs68070528	0.84[ASN][1000 genomes]
rs73066671	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8112238	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9676909	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55685200-55690400	Weak transcription	Gastric	stomach
2	chr19:55685600-55690400	Weak transcription	Pancreas	Pancrea
3	chr19:55685600-55690400	Weak transcription	Right Atrium	heart
4	chr19:55685800-55690200	Weak transcription	Osteobl	bone
5	chr19:55685800-55690400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:55686000-55690200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:55686000-55690200	Weak transcription	A549	lung
8	chr19:55686000-55690200	Weak transcription	NHEK	skin
9	chr19:55688000-55690200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:55688600-55690200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:55689200-55691200	Enhancers	Primary hematopoietic stem cells	blood
12	chr19:55689200-55691200	Enhancers	Hela-S3	cervix
13	chr19:55689400-55690200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:55689600-55690200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:55689600-55690200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:55689600-55690200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr19:55689600-55690200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
18	chr19:55689600-55690200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
19	chr19:55689600-55690200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:55689600-55690200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:55689600-55690200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr19:55689600-55690400	Enhancers	Fetal Brain Male	brain
23	chr19:55689800-55690200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:55689800-55690200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:55689800-55690200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr19:55689800-55690200	Flanking Active TSS	Brain Germinal Matrix	brain
27	chr19:55689800-55690200	Bivalent Enhancer	Fetal Thymus	thymus
28	chr19:55689800-55690200	Bivalent Enhancer	Thymus	Thymus
29	chr19:55689800-55690400	Bivalent Enhancer	Primary B cells from cord blood	blood
30	chr19:55689800-55690400	Enhancers	K562	blood
31	chr19:55689800-55690600	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr19:55689800-55690800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr19:55689800-55691000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:55689800-55691000	Active TSS	Brain Cingulate Gyrus	brain
35	chr19:55690000-55690200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr19:55690000-55690200	Active TSS	Brain Angular Gyrus	brain
37	chr19:55690000-55690200	Enhancers	GM12878-XiMat	blood
38	chr19:55690000-55690400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:55690000-55690400	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr19:55690000-55690400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:55690000-55690400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:55690000-55690400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
43	chr19:55690000-55690400	Bivalent Enhancer	Brain Substantia Nigra	brain
44	chr19:55690000-55690600	Active TSS	Primary T cells from cord blood	blood
45	chr19:55690000-55690600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:55690000-55690600	Bivalent Enhancer	Fetal Stomach	stomach
47	chr19:55690000-55690800	Flanking Active TSS	Dnd41	blood
48	chr19:55690000-55691000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:55690000-55691000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr19:55690000-55691000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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