Variant report

Variant	rs11083489
Chromosome Location	chr19:39409236-39409237
allele	A/C
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	chr19:39408099-39409398	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:39407747-39409674	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:39408887-39409467	A549	lung:	n/a	n/a
4	CTCF	chr19:39408445-39409548	A549	lung:	n/a	chr19:39408855-39408864
5	POLR2A	chr19:39408945-39409414	K562	blood:	n/a	n/a
6	POLR2A	chr19:39408933-39409364	K562	blood:	n/a	n/a
7	ZNF263	chr19:39408706-39409382	HEK293-T-REx	kidney:	n/a	chr19:39409014-39409035 chr19:39409245-39409254 chr19:39409031-39409040 chr19:39409174-39409183
8	POLR2A	chr19:39408330-39409602	A549	lung:	n/a	n/a
9	POLR2A	chr19:39402657-39410674	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr19:39407758-39409703	K562	blood:	n/a	n/a
11	POLR2A	chr19:39409018-39409261	ECC-1	luminal epithelium:	n/a	n/a
12	BCL3	chr19:39408389-39409295	A549	lung:	n/a	n/a
13	POLR2A	chr19:39409079-39409283	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:39399024-39410741	PANC-1	pancreas:	n/a	n/a
15	NR2F2	chr19:39408514-39409348	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39340110..39342981-chr19:39406423..39409674,4	MCF-7	breast:
2	chr19:39388836..39392687-chr19:39409083..39412619,5	K562	blood:
3	chr19:39369301..39370035-chr19:39408587..39409292,2	MCF-7	breast:
4	chr19:39332878..39335584-chr19:39408217..39410062,2	MCF-7	breast:

Variant related genes	Relation type
SARS2	TF binding region
ENSG00000068903	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000104825	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10410544	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10416055	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425217	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10426382	1.00[JPT][hapmap]
rs10775533	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083488	0.92[EUR][1000 genomes]
rs11668245	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462710	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609975	0.85[EUR][1000 genomes]
rs12610409	0.92[ASN][1000 genomes]
rs12972986	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979755	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12985428	0.82[EUR][1000 genomes]
rs17545254	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808661	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1808662	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865047	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865049	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2278412	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs3136640	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs4801960	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4801971	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802998	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4803006	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4803034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257007	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730078	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7508411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508539	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113389	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9636109	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9749516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11083489	SARS2	cis	multi-tissue	Pritchard
rs11083489	MYPOP	cis	parietal	SCAN
rs11083489	PLD3	cis	parietal	SCAN
rs11083489	SARS2	cis	lymphoblastoid	seeQTL
rs11083489	LGALS14	cis	parietal	SCAN
rs11083489	CTC-360G5.9	cis	Nerve Tibial	GTEx
rs11083489	GPR4	cis	parietal	SCAN
rs11083489	PRR19	cis	parietal	SCAN
rs11083489	ZNF285	cis	cerebellum	SCAN

Chromatin state (count:116 , 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	chr19:39392600-39414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr19:39395600-39414800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:39395600-39415000	Weak transcription	Hela-S3	cervix
10	chr19:39396800-39412000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:39397000-39412200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:39398000-39412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
14	chr19:39398200-39412200	Weak transcription	Brain Angular Gyrus	brain
15	chr19:39398400-39411600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:39398600-39410200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:39398600-39415000	Weak transcription	Brain Substantia Nigra	brain
18	chr19:39398800-39410000	Weak transcription	HSMMtube	muscle
19	chr19:39398800-39411600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:39398800-39412000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr19:39398800-39412200	Weak transcription	NHEK	skin
22	chr19:39398800-39412400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr19:39398800-39415000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:39399000-39412400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:39399800-39412200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:39399800-39412200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr19:39399800-39414800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr19:39399800-39414800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:39400000-39410000	Weak transcription	K562	blood
30	chr19:39400000-39412000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr19:39400000-39412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:39400000-39412200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:39400000-39412200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr19:39400000-39412200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:39400000-39414200	Weak transcription	Left Ventricle	heart
36	chr19:39400200-39410000	Weak transcription	Primary T cells from cord blood	blood
37	chr19:39400200-39410000	Weak transcription	Dnd41	blood
38	chr19:39400200-39412000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr19:39400200-39412000	Weak transcription	Aorta	Aorta
40	chr19:39400200-39412600	Weak transcription	Primary B cells from cord blood	blood
41	chr19:39400200-39412800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:39401000-39412000	Weak transcription	Gastric	stomach
43	chr19:39402400-39412200	Weak transcription	Right Ventricle	heart
44	chr19:39402800-39420200	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:39403000-39412000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:39403000-39412000	Weak transcription	NHLF	lung
47	chr19:39403000-39412400	Weak transcription	Fetal Thymus	thymus
48	chr19:39403000-39415000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:39403400-39412000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:39403400-39412200	Weak transcription	Brain Anterior Caudate	brain

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