Variant report

Variant	rs73062564
Chromosome Location	chr19:56207872-56207873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56207633-56208369	HL-60	blood:	n/a	n/a
2	POLR2A	chr19:56207572-56208310	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:56207407-56208822	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:56207524-56207951	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:56206989-56208090	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:56207256-56208719	GM19193	blood:	n/a	n/a
7	POLR2A	chr19:56207166-56208372	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:56206468-56210085	K562	blood:	n/a	n/a
9	POLR2A	chr19:56207156-56208891	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:56207579-56208622	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:56207160-56208116	K562	blood:	n/a	n/a
12	POLR2A	chr19:56207153-56208168	GM18505	blood:	n/a	n/a
13	POLR2A	chr19:56206908-56208637	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:56207682-56208650	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:56207063-56208730	GM12892	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56194595..56204961-chr19:56206160..56210902,10	K562	blood:
2	chr19:56189741..56193540-chr19:56204383..56209311,7	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPN1-2	chr19:56207681-56208795	ENSG00000267018.1

No data

Variant related genes	Relation type
ENSG00000267117	TF binding region
ENSG00000203305	TF binding region
ENSG00000211571	Chromatin interaction
ENSG00000063245	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10419814	0.80[EUR][1000 genomes]
rs11084406	1.00[ASN][1000 genomes]
rs11665772	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11665872	1.00[ASN][1000 genomes]
rs11666362	1.00[ASN][1000 genomes]
rs11668830	0.81[AMR][1000 genomes]
rs11671023	1.00[ASN][1000 genomes]
rs11882068	0.84[AMR][1000 genomes]
rs2112799	1.00[ASN][1000 genomes]
rs28527338	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3786650	1.00[ASN][1000 genomes]
rs4541174	1.00[ASN][1000 genomes]
rs4801261	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59900917	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73062405	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73062531	1.00[ASN][1000 genomes]
rs8104386	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	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	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
5	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
6	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
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73062564	ZNF580	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:56188600-56210000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
7	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
8	chr19:56189000-56210000	Strong transcription	Fetal Brain Female	brain
9	chr19:56189200-56209400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:56189200-56212600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr19:56189400-56209400	Strong transcription	Fetal Thymus	thymus
12	chr19:56189400-56209400	Strong transcription	Dnd41	blood
13	chr19:56189400-56212400	Strong transcription	Brain Germinal Matrix	brain
14	chr19:56189600-56209400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:56189600-56209800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr19:56189600-56213200	Strong transcription	Primary T cells from cord blood	blood
17	chr19:56190000-56212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:56190200-56210200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:56190200-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:56191000-56212400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:56191800-56218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:56192000-56214600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr19:56192200-56209800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:56192200-56211200	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:56192400-56212400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:56192600-56209200	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:56192800-56213200	Strong transcription	Adipose Nuclei	Adipose
28	chr19:56193200-56214000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:56193600-56213200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:56193800-56212000	Weak transcription	HSMM	muscle
31	chr19:56194000-56209600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:56194600-56209800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:56194800-56208400	Strong transcription	NHLF	lung
34	chr19:56195000-56208400	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr19:56195000-56210000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:56195000-56210200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr19:56195000-56212400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:56195400-56208000	Weak transcription	Fetal Kidney	kidney
39	chr19:56195400-56217600	Weak transcription	Right Atrium	heart
40	chr19:56195800-56210000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr19:56196000-56208000	Strong transcription	Fetal Lung	lung
42	chr19:56196200-56210200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr19:56196400-56210000	Strong transcription	Left Ventricle	heart
44	chr19:56197600-56212600	Strong transcription	Lung	lung
45	chr19:56197800-56212400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:56198800-56208400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr19:56199000-56209400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:56199000-56212400	Strong transcription	Liver	Liver
49	chr19:56199200-56210800	Strong transcription	Pancreas	Pancrea
50	chr19:56199200-56214600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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