Variant report

Variant	rs4803027
Chromosome Location	chr19:39404800-39404801
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39404322-39405101	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:39404789-39405161	K562	blood:	n/a	n/a
3	POLR2A	chr19:39404716-39404893	HCT-116	colon:	n/a	n/a
4	POLR2A	chr19:39404432-39405198	K562	blood:	n/a	n/a
5	POLR2A	chr19:39404437-39404920	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr19:39404306-39405201	K562	blood:	n/a	n/a
7	BCL3	chr19:39404416-39404929	A549	lung:	n/a	n/a
8	POLR2A	chr19:39402657-39410674	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr19:39404639-39404857	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:39399024-39410741	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:39404613-39405388	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39339767..39341589-chr19:39404601..39407841,3	K562	blood:
2	chr19:39340089..39343125-chr19:39404601..39408323,3	K562	blood:
3	chr19:39384229..39386196-chr19:39403385..39405980,2	K562	blood:
4	chr19:39398169..39400794-chr19:39403289..39404909,2	MCF-7	breast:
5	chr19:39402244..39405531-chr19:39405569..39407779,3	MCF-7	breast:

No data

Variant related genes	Relation type
CCER2	TF binding region
ENSG00000104835	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000068903	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs12971945	0.81[ASN][1000 genomes]
rs12975517	0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12977011	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12985277	0.84[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12985768	0.89[ASN][1000 genomes]
rs4803028	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs733084	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4803027	SARS2	cis	lymphoblastoid	seeQTL
rs4803027	APOC4	cis	cerebellum	SCAN
rs4803027	PHLDB3	cis	cerebellum	SCAN
rs4803027	ZNF526	cis	parietal	SCAN
rs4803027	PLD3	cis	parietal	SCAN
rs4803027	DEDD2	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391600-39414800	Weak transcription	HMEC	breast
3	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
4	chr19:39391800-39412200	Weak transcription	Osteobl	bone
5	chr19:39392400-39414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:39392600-39406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:39392600-39414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:39395600-39414800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:39395600-39415000	Weak transcription	Hela-S3	cervix
11	chr19:39396600-39408400	Weak transcription	HepG2	liver
12	chr19:39396800-39412000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:39397000-39412200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:39398000-39412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
16	chr19:39398200-39412200	Weak transcription	Brain Angular Gyrus	brain
17	chr19:39398400-39411600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:39398600-39410200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:39398600-39415000	Weak transcription	Brain Substantia Nigra	brain
20	chr19:39398800-39409000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:39398800-39410000	Weak transcription	HSMMtube	muscle
22	chr19:39398800-39411600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:39398800-39412000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr19:39398800-39412200	Weak transcription	NHEK	skin
25	chr19:39398800-39412400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:39398800-39415000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:39399000-39412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:39399800-39408400	Weak transcription	A549	lung
29	chr19:39399800-39409000	Weak transcription	Pancreas	Pancrea
30	chr19:39399800-39412200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:39399800-39412200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr19:39399800-39414800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr19:39399800-39414800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:39400000-39405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:39400000-39405800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:39400000-39405800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:39400000-39410000	Weak transcription	K562	blood
38	chr19:39400000-39412000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr19:39400000-39412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr19:39400000-39412200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr19:39400000-39412200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:39400000-39412200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:39400000-39414200	Weak transcription	Left Ventricle	heart
44	chr19:39400200-39405800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:39400200-39405800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:39400200-39405800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr19:39400200-39405800	Weak transcription	Liver	Liver
48	chr19:39400200-39405800	Weak transcription	Lung	lung
49	chr19:39400200-39406000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:39400200-39406200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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