Variant report

Variant	rs60345290
Chromosome Location	chr19:55691580-55691581
allele	G/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	chr19:55691407-55691711	HepG2	liver:	n/a	chr19:55691555-55691562 chr19:55691556-55691565 chr19:55691458-55691468 chr19:55691554-55691564
2	REST	chr19:55691277-55691905	PFSK-1	brain:	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
3	REST	chr19:55691191-55692010	MCF-7	breast:	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
4	RCOR1	chr19:55691430-55691752	GM12878	blood:	n/a	n/a
5	UBTF	chr19:55691438-55691714	K562	blood:	n/a	n/a
6	JUN	chr19:55691392-55691718	K562	blood:	n/a	n/a
7	MAX	chr19:55691336-55691806	HepG2	liver:	n/a	chr19:55691737-55691747 chr19:55691555-55691562 chr19:55691556-55691565 chr19:55691458-55691468 chr19:55691554-55691564
8	MXI1	chr19:55691376-55691783	HepG2	liver:	n/a	n/a
9	REST	chr19:55691408-55691738	GM12878	blood:	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
10	REST	chr19:55691009-55692127	MCF-7	breast:	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
11	MAX	chr19:55691203-55691848	HCT-116	colon:	n/a	chr19:55691737-55691747 chr19:55691555-55691562 chr19:55691556-55691565 chr19:55691458-55691468 chr19:55691554-55691564
12	E2F6	chr19:55691451-55691714	K562	blood:	n/a	n/a
13	JUN	chr19:55689997-55692239	K562	blood:	n/a	chr19:55690959-55690968 chr19:55690279-55690293
14	FOXA1	chr19:55691447-55691790	HepG2	liver:	n/a	n/a
15	RCOR1	chr19:55691380-55691777	K562	blood:	n/a	n/a
16	USF1	chr19:55691386-55691713	A549	lung:	n/a	chr19:55691570-55691586
17	REST	chr19:55691318-55691721	HepG2	liver:	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
18	REST	chr19:55691275-55691814	U87	brain:	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
19	CHD2	chr19:55691363-55691601	Hela-S3	cervix:	n/a	n/a
20	ZNF143	chr19:55691438-55691695	K562	blood:	n/a	n/a
21	EGR1	chr19:55691311-55691900	K562	blood:	n/a	chr19:55691556-55691566 chr19:55691555-55691569 chr19:55691554-55691567 chr19:55691740-55691753 chr19:55691602-55691615 chr19:55691556-55691566 chr19:55691557-55691566 chr19:55691554-55691568 chr19:55691560-55691567
22	BCL3	chr19:55691224-55691860	K562	blood:	n/a	chr19:55691602-55691611
23	HMGN3	chr19:55691347-55691784	K562	blood:	n/a	n/a
24	REST	chr19:55690386-55692323	PFSK-1	brain:	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
25	SIN3AK20	chr19:55691333-55691715	A549	lung:	n/a	n/a
26	USF1	chr19:55691355-55691791	SK-N-SH_RA	brain:	n/a	chr19:55691570-55691586
27	USF1	chr19:55691450-55691690	GM12878	blood:	n/a	chr19:55691570-55691586
28	SIN3AK20	chr19:55690648-55691885	PANC-1	pancreas:	n/a	n/a
29	RCOR1	chr19:55691471-55691718	HepG2	liver:	n/a	n/a
30	USF2	chr19:55691412-55691718	GM12878	blood:	n/a	chr19:55691570-55691586
31	NR2F2	chr19:55691455-55691831	K562	blood:	n/a	n/a
32	SMC3	chr19:55691559-55691648	Hela-S3	cervix:	n/a	n/a
33	REST	chr19:55690984-55692047	HL-60	blood:	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
34	REST	chr19:55690261-55692603	PANC-1	pancreas:	n/a	chr19:55691568-55691588 chr19:55692420-55692429 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
35	ZBTB7A	chr19:55691360-55691659	K562	blood:	n/a	n/a
36	MYC	chr19:55691553-55691599	MCF10A-Er-Src	breast:	n/a	chr19:55691555-55691562 chr19:55691556-55691565 chr19:55691554-55691564
37	MAZ	chr19:55691412-55691703	HepG2	liver:	n/a	chr19:55691555-55691562 chr19:55691556-55691565 chr19:55691458-55691468 chr19:55691554-55691564
38	EGR1	chr19:55691423-55691690	GM12878	blood:	n/a	chr19:55691556-55691566 chr19:55691555-55691569 chr19:55691554-55691567 chr19:55691602-55691615 chr19:55691556-55691566 chr19:55691557-55691566 chr19:55691554-55691568 chr19:55691560-55691567
39	USF1	chr19:55691448-55691689	GM12878	blood:	n/a	chr19:55691570-55691586
40	REST	chr19:55691444-55691651	PANC-1	pancreas:	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
41	JUND	chr19:55691462-55691602	H1-hESC	embryonic stem cell:	n/a	n/a
42	REST	chr19:55691282-55691871	GM12878	blood:	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
43	POLR2A	chr19:55691367-55691895	K562	blood:	n/a	n/a
44	POLR2A	chr19:55690065-55692089	H1-neurons	neurons:	n/a	n/a
45	ZC3H11A	chr19:55691573-55691663	K562	blood:	n/a	n/a
46	TAF1	chr19:55690154-55691948	H1-neurons	neurons:	n/a	n/a
47	REST	chr19:55691156-55692127	GM12878	blood:	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
48	MYBL2	chr19:55691273-55691636	HepG2	liver:	n/a	n/a
49	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
50	REST	chr19:55691275-55691925	PANC-1	pancreas:	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

No.	Distal block	Cell Line	Cell type
1	chr19:55690523..55693470-chr19:55767618..55771014,3	K562	blood:
2	chr19:55688939..55693251-chr19:55917287..55920595,8	K562	blood:
3	chr19:55689704..55692023-chr19:55769514..55771598,2	K562	blood:
4	chr19:55690071..55692651-chr19:55739628..55742521,2	MCF-7	breast:
5	chr19:55688567..55692973-chr19:55725028..55730023,9	K562	blood:
6	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:
7	chr19:55689066..55691659-chr19:55726623..55728296,2	MCF-7	breast:
8	chr19:55688770..55691626-chr19:55917418..55920191,3	K562	blood:
9	chr19:55690189..55693086-chr19:55769247..55770801,2	MCF-7	breast:
10	chr19:55690042..55692776-chr19:55717237..55718780,2	K562	blood:
11	chr19:55688544..55691824-chr19:55726439..55729589,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55691523-55695370	l_1714_chr19:55688749-55693967_brain

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

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56118388	0.84[AFR][1000 genomes]
rs56740066	0.81[AFR][1000 genomes]
rs58160126	0.84[AFR][1000 genomes]
rs58893984	0.81[AFR][1000 genomes]
rs73619544	1.00[EUR][1000 genomes]
rs73935321	0.84[AFR][1000 genomes]
rs73935322	0.81[AFR][1000 genomes]
rs73935323	0.81[AFR][1000 genomes]
rs73935324	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55690000-55691600	Active TSS	Brain Anterior Caudate	brain
2	chr19:55690200-55691600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:55690200-55691600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr19:55690200-55691600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:55690200-55691600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:55690200-55691600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
7	chr19:55690200-55691600	Flanking Bivalent TSS/Enh	Thymus	Thymus
8	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
9	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:55690200-55691800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:55690200-55691800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
12	chr19:55690200-55691800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr19:55690200-55692000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr19:55690200-55692000	Bivalent Enhancer	Placenta	Placenta
15	chr19:55690200-55692200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:55690400-55691600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr19:55690400-55691600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:55690400-55692000	Enhancers	Gastric	stomach
19	chr19:55690600-55691600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr19:55690600-55691600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr19:55690600-55691600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr19:55690600-55691600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:55690600-55691800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
24	chr19:55690600-55691800	Active TSS	Brain Angular Gyrus	brain
25	chr19:55690600-55691800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
26	chr19:55690600-55691800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr19:55690600-55692000	Bivalent Enhancer	Lung	lung
28	chr19:55690800-55691600	Bivalent Enhancer	Left Ventricle	heart
29	chr19:55690800-55691600	Enhancers	Placenta Amnion	Placenta Amnion
30	chr19:55690800-55691800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:55690800-55691800	Bivalent Enhancer	Esophagus	oesophagus
32	chr19:55690800-55691800	Enhancers	Dnd41	blood
33	chr19:55690800-55692000	Enhancers	Fetal Heart	heart
34	chr19:55691000-55691600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:55691000-55691600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:55691000-55691600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
37	chr19:55691000-55691600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:55691000-55691600	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr19:55691000-55691800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:55691000-55691800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
41	chr19:55691000-55691800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
42	chr19:55691000-55691800	Bivalent Enhancer	Fetal Thymus	thymus
43	chr19:55691000-55691800	Bivalent Enhancer	Spleen	Spleen
44	chr19:55691000-55691800	Flanking Bivalent TSS/Enh	A549	lung
45	chr19:55691000-55692000	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr19:55691000-55692200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr19:55691200-55691600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
48	chr19:55691200-55691800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:55691200-55692000	Bivalent/Poised TSS	Fetal Brain Female	brain
50	chr19:55691200-55692000	Flanking Active TSS	Hela-S3	cervix

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