Variant report

Variant	rs519856
Chromosome Location	chr19:56162881-56162882
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	chr19:56162315-56163146	K562	blood:	n/a	n/a
2	POLR2A	chr19:56162732-56163017	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56110653..56113509-chr19:56160158..56165183,5	MCF-7	breast:
2	chr19:56134460..56137185-chr19:56162633..56166165,3	K562	blood:
3	chr19:56134221..56137618-chr19:56162633..56168532,10	K562	blood:

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000171443	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000179922	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1808393	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2864434	0.90[ASN][1000 genomes]
rs310436	0.84[ASN][1000 genomes]
rs485152	0.91[ASN][1000 genomes]
rs504850	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579496	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs596075	0.89[ASN][1000 genomes]
rs643368	0.91[ASN][1000 genomes]
rs664684	0.87[ASN][1000 genomes]
rs7247677	0.86[ASN][1000 genomes]
rs7249837	0.81[ASN][1000 genomes]
rs7252055	0.90[ASN][1000 genomes]
rs889092	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
5	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
7	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs519856	ZNF580	cis	Artery Tibial	GTEx
rs519856	ZNF580	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56160000-56165200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:56160200-56165200	Weak transcription	Small Intestine	intestine
3	chr19:56160400-56163200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:56160400-56163400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:56160400-56163400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:56160400-56163400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:56160400-56164200	Weak transcription	Psoas Muscle	Psoas
8	chr19:56160400-56164400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:56160400-56164400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:56160400-56164400	Weak transcription	NHEK	skin
11	chr19:56160400-56165000	Weak transcription	HSMMtube	muscle
12	chr19:56160400-56165200	Weak transcription	NHDF-Ad	bronchial
13	chr19:56160600-56163200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:56160600-56163400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:56160600-56164000	Weak transcription	Fetal Heart	heart
16	chr19:56160600-56164200	Weak transcription	HMEC	breast
17	chr19:56160600-56164400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr19:56160600-56164600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:56160600-56164600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:56160600-56164600	Weak transcription	Osteobl	bone
21	chr19:56160600-56164800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:56160800-56163000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:56160800-56163400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr19:56160800-56163600	Weak transcription	Brain Germinal Matrix	brain
25	chr19:56160800-56163600	Weak transcription	Fetal Intestine Large	intestine
26	chr19:56160800-56164200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:56160800-56164400	Weak transcription	Hela-S3	cervix
28	chr19:56160800-56164400	Weak transcription	HepG2	liver
29	chr19:56160800-56164600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:56160800-56164600	Strong transcription	NHLF	lung
31	chr19:56160800-56164800	Weak transcription	Fetal Lung	lung
32	chr19:56160800-56165000	Weak transcription	Liver	Liver
33	chr19:56160800-56165200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr19:56160800-56165200	Weak transcription	Gastric	stomach
35	chr19:56160800-56165200	Weak transcription	Left Ventricle	heart
36	chr19:56160800-56165200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:56161000-56163200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:56161000-56163400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:56161000-56163400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:56161000-56163400	Weak transcription	A549	lung
41	chr19:56161000-56163800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:56161000-56164200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:56161000-56164200	Strong transcription	Fetal Intestine Small	intestine
44	chr19:56161000-56164400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:56161000-56164400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:56161000-56164600	Weak transcription	Adipose Nuclei	Adipose
47	chr19:56161000-56164600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr19:56161000-56164600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr19:56161000-56164800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:56161000-56164800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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