Variant report

Variant	rs55874363
Chromosome Location	chr19:56907158-56907159
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	USF1	chr19:56907135-56907355	HepG2	liver:	n/a	chr19:56907269-56907280
2	FOSL2	chr19:56907054-56907403	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:56906996-56907326	GM12878	blood:	n/a	n/a
4	USF1	chr19:56907112-56907363	GM12878	blood:	n/a	chr19:56907269-56907280

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56902006..56908060-chr19:56909612..56917978,15	K562	blood:

Variant related genes	Relation type
ZNF582	TF binding region
ZNF583	TF binding region
ENSG00000198440	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11084446	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12608966	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12610115	0.82[EUR][1000 genomes]
rs35080747	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56301546	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59858465	0.84[EUR][1000 genomes]
rs7258010	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8102580	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv544096	chr19:56905651-56933455	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55874363	ZNF582-AS1	cis	Adipose Subcutaneous	GTEx
rs55874363	ZNF582-AS1	cis	lung	GTEx
rs55874363	ZNF582-AS1	cis	Artery Tibial	GTEx
rs55874363	ZNF582-AS1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56905000-56913600	ZNF genes & repeats	Liver	Liver
2	chr19:56905400-56909000	Weak transcription	Spleen	Spleen
3	chr19:56905400-56909200	Weak transcription	Ovary	ovary
4	chr19:56905400-56909400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:56905400-56910800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:56905400-56911000	Weak transcription	Stomach Mucosa	stomach
7	chr19:56905600-56908400	Weak transcription	Primary T cells from cord blood	blood
8	chr19:56905600-56908400	Weak transcription	HSMMtube	muscle
9	chr19:56905600-56908800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:56905600-56909200	Weak transcription	Aorta	Aorta
11	chr19:56905600-56909400	Weak transcription	Brain Germinal Matrix	brain
12	chr19:56905600-56909400	Weak transcription	Brain Substantia Nigra	brain
13	chr19:56905600-56909400	Weak transcription	Fetal Brain Female	brain
14	chr19:56905600-56910000	Weak transcription	Fetal Brain Male	brain
15	chr19:56905600-56910200	Weak transcription	Fetal Kidney	kidney
16	chr19:56905600-56914600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr19:56905800-56907400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:56905800-56908600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:56905800-56908800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:56905800-56908800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:56905800-56908800	Weak transcription	Brain Hippocampus Middle	brain
22	chr19:56905800-56909000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr19:56905800-56909000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr19:56905800-56909000	Weak transcription	Fetal Muscle Leg	muscle
25	chr19:56905800-56909000	Weak transcription	Fetal Stomach	stomach
26	chr19:56905800-56909000	Weak transcription	Left Ventricle	heart
27	chr19:56905800-56909200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:56905800-56909200	Weak transcription	Colon Smooth Muscle	Colon
29	chr19:56905800-56909200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr19:56905800-56909200	Weak transcription	Fetal Lung	lung
31	chr19:56905800-56910000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:56905800-56914400	Weak transcription	Fetal Heart	heart
33	chr19:56906000-56908800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:56906000-56908800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr19:56906000-56909400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:56906000-56909400	Weak transcription	Right Ventricle	heart
37	chr19:56906000-56910200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:56906000-56910200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:56906000-56910400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr19:56906200-56909000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr19:56906200-56909200	Weak transcription	Brain Anterior Caudate	brain
42	chr19:56906200-56909400	Weak transcription	Brain Angular Gyrus	brain
43	chr19:56906200-56909400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr19:56906400-56907200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:56906400-56907200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
46	chr19:56906400-56908200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:56906600-56908000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:56906600-56909000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr19:56907000-56908000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr19:56907000-56908800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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