Variant report

Variant	rs56720219
Chromosome Location	chr19:52205652-52205653
allele	A/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	POLR2A	chr19:52205081-52208349	K562	blood:	n/a	n/a
2	POLR2A	chr19:52205472-52206489	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr19:52205228-52208187	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr19:52204903-52210059	K562	blood:	n/a	n/a
5	POLR2A	chr19:52205403-52206809	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZMIZ1	chr19:52205465-52205855	K562	blood:	n/a	n/a
7	POLR2A	chr19:52205267-52208184	MCF-7	breast:	n/a	n/a
8	POLR2A	chr19:52204570-52209007	K562	blood:	n/a	n/a
9	POLR2A	chr19:52205512-52205884	ProgFib	skin:	n/a	n/a
10	ZNF143	chr19:52205597-52205966	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr19:52205566-52205998	MCF-7	breast:	n/a	n/a
12	POLR2A	chr19:52205175-52208963	PFSK-1	brain:	n/a	n/a
13	JUND	chr19:52204803-52205947	K562	blood:	n/a	n/a
14	MAZ	chr19:52204752-52207931	K562	blood:	n/a	chr19:52206354-52206364 chr19:52205773-52205783
15	HEY1	chr19:52205525-52205938	K562	blood:	n/a	n/a
16	ZBTB7A	chr19:52205205-52205870	K562	blood:	n/a	chr19:52205438-52205445
17	MAX	chr19:52205541-52206665	H1-hESC	embryonic stem cell:	n/a	chr19:52206354-52206364 chr19:52205773-52205783
18	CREB1	chr19:52205547-52205973	A549	lung:	n/a	n/a
19	NR2F2	chr19:52204830-52206006	K562	blood:	n/a	n/a
20	MYC	chr19:52204843-52205951	K562	blood:	n/a	chr19:52205773-52205783
21	SIN3A	chr19:52205323-52206773	H1-hESC	embryonic stem cell:	n/a	n/a
22	SP1	chr19:52205528-52205953	H1-hESC	embryonic stem cell:	n/a	chr19:52205741-52205751 chr19:52205567-52205579 chr19:52205770-52205781 chr19:52205771-52205780 chr19:52205770-52205782 chr19:52205567-52205579 chr19:52205741-52205751 chr19:52205740-52205752 chr19:52205569-52205578 chr19:52205771-52205785 chr19:52205770-52205782 chr19:52205741-52205750 chr19:52205740-52205752 chr19:52205771-52205781 chr19:52205771-52205780 chr19:52205568-52205582 chr19:52205741-52205750 chr19:52205772-52205781 chr19:52205742-52205751 chr19:52205568-52205577 chr19:52205771-52205781
23	MAX	chr19:52205468-52206712	H1-hESC	embryonic stem cell:	n/a	chr19:52206354-52206364 chr19:52205773-52205783
24	POLR2A	chr19:52205075-52207903	PANC-1	pancreas:	n/a	n/a
25	CREB1	chr19:52205558-52206365	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F6	chr19:52205543-52207126	H1-hESC	embryonic stem cell:	n/a	chr19:52205772-52205781 chr19:52205569-52205578 chr19:52205742-52205751 chr19:52206601-52206611 chr19:52206356-52206365
27	EGR1	chr19:52205586-52205897	K562	blood:	n/a	chr19:52205773-52205786 chr19:52205771-52205781
28	POLR2A	chr19:52205153-52209028	U87	brain:	n/a	n/a
29	POLR2A	chr19:52205408-52207877	PANC-1	pancreas:	n/a	n/a
30	CEBPB	chr19:52205619-52206000	A549	lung:	n/a	n/a
31	POLR2A	chr19:52205382-52207928	HUVEC	blood vessel:	n/a	n/a
32	TAF1	chr19:52205385-52205907	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr19:52205529-52206010	A549	lung:	n/a	n/a
34	POLR2A	chr19:52205475-52205795	ECC-1	luminal epithelium:	n/a	n/a
35	IRF1	chr19:52204975-52206052	K562	blood:	n/a	chr19:52205431-52205445 chr19:52205768-52205782 chr19:52205497-52205511 chr19:52205565-52205579 chr19:52205738-52205752
36	POLR2A	chr19:52205436-52205951	HCT-116	colon:	n/a	n/a
37	CEBPB	chr19:52205518-52205985	K562	blood:	n/a	n/a
38	CEBPB	chr19:52205630-52205945	IMR90	lung:	n/a	n/a
39	POLR2A	chr19:52204333-52208183	SK-N-MC	brain:	n/a	n/a
40	BCL3	chr19:52205649-52206142	A549	lung:	n/a	n/a
41	POLR2A	chr19:52205547-52205940	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr19:52205489-52209077	U87	brain:	n/a	n/a
43	TAF1	chr19:52205547-52205737	H1-hESC	embryonic stem cell:	n/a	n/a
44	E2F6	chr19:52205628-52205818	K562	blood:	n/a	chr19:52205772-52205781 chr19:52205742-52205751
45	TBL1XR1	chr19:52205577-52205795	K562	blood:	n/a	n/a
46	CREB1	chr19:52205423-52206207	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr19:52205499-52205973	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr19:52205441-52206047	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr19:52204780-52207896	K562	blood:	n/a	n/a
50	CEBPB	chr19:52205583-52205922	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52204118..52207726-chr19:52271324..52274498,3	K562	blood:
2	chr19:52196159..52199511-chr19:52202868..52206043,4	K562	blood:

Variant related genes	Relation type
SPACA6P	TF binding region
ENSG00000182310	Chromatin interaction
ENSG00000208008	Chromatin interaction
ENSG00000273318	Chromatin interaction
ENSG00000269959	Chromatin interaction
ENSG00000171049	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10408429	0.98[ASN][1000 genomes]
rs10422727	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16982947	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2122893	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290282	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28473660	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73054883	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73054899	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	esv1843680	chr19:52131510-52211749	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
12	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	518 gene(s)	inside rSNPs	diseases
13	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
14	nsv9742	chr19:52187538-52221742	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	517 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52194600-52205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:52194600-52207000	Weak transcription	Psoas Muscle	Psoas
3	chr19:52195000-52205800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:52195000-52205800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr19:52195200-52205800	Weak transcription	Primary T cells from cord blood	blood
6	chr19:52195400-52207200	Weak transcription	Hela-S3	cervix
7	chr19:52196400-52206400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:52196400-52206600	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr19:52196600-52205800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr19:52197000-52205800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:52200200-52206000	Strong transcription	HUVEC	blood vessel
12	chr19:52202000-52205800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:52202000-52206800	Strong transcription	Osteobl	bone
14	chr19:52202200-52205800	Weak transcription	Brain Substantia Nigra	brain
15	chr19:52202400-52205800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr19:52202400-52206000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:52202400-52207200	Weak transcription	Aorta	Aorta
18	chr19:52202600-52205800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:52202600-52206800	Weak transcription	Fetal Brain Male	brain
20	chr19:52203000-52205800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:52203000-52206800	Weak transcription	NHDF-Ad	bronchial
22	chr19:52203000-52207200	Weak transcription	HSMMtube	muscle
23	chr19:52203800-52205800	Weak transcription	Ovary	ovary
24	chr19:52204000-52206600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:52204400-52205800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr19:52204400-52206000	Genic enhancers	Placenta	Placenta
27	chr19:52204400-52208600	Enhancers	Fetal Heart	heart
28	chr19:52204600-52205800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:52204600-52205800	Enhancers	Pancreas	Pancrea
30	chr19:52204600-52206400	Enhancers	Gastric	stomach
31	chr19:52204600-52206800	Enhancers	Right Atrium	heart
32	chr19:52204600-52206800	Strong transcription	NHLF	lung
33	chr19:52204800-52206800	Flanking Active TSS	K562	blood
34	chr19:52204800-52207000	Genic enhancers	A549	lung
35	chr19:52204800-52208000	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr19:52204800-52208200	Active TSS	H9 Cell Line	embryonic stem cell
37	chr19:52205000-52206600	Weak transcription	Fetal Kidney	kidney
38	chr19:52205000-52208000	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr19:52205000-52208400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr19:52205200-52205800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr19:52205200-52205800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:52205200-52205800	Weak transcription	Adipose Nuclei	Adipose
43	chr19:52205200-52206000	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr19:52205200-52206000	Enhancers	Esophagus	oesophagus
45	chr19:52205200-52206000	Enhancers	Stomach Mucosa	stomach
46	chr19:52205200-52206200	Genic enhancers	Fetal Muscle Leg	muscle
47	chr19:52205200-52206400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:52205200-52206400	Enhancers	Brain Germinal Matrix	brain
49	chr19:52205200-52206400	Enhancers	Spleen	Spleen
50	chr19:52205200-52206400	Strong transcription	HSMM	muscle

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