Variant report

Variant	rs575
Chromosome Location	chr19:39432783-39432784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39432500-39432885	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr19:39432691-39432903	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:39432688-39433853	K562	blood:	n/a	n/a
4	POLR2A	chr19:39428658-39436712	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:39432429-39433883	HepG2	liver:	n/a	n/a
6	FOSL2	chr19:39432505-39433892	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:39432384-39433818	K562	blood:	n/a	n/a
8	POLR2A	chr19:39432502-39432882	U87	brain:	n/a	n/a
9	POLR2A	chr19:39432613-39432986	U87	brain:	n/a	n/a
10	POLR2A	chr19:39428415-39444124	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:39432614-39432900	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:39432173-39442255	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:39432667-39432877	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3AK20	chr19:39432455-39433893	PANC-1	pancreas:	n/a	n/a
15	SIN3AK20	chr19:39432644-39433727	PANC-1	pancreas:	n/a	n/a
16	BCL3	chr19:39432241-39434020	A549	lung:	n/a	n/a
17	BCL3	chr19:39432429-39433634	A549	lung:	n/a	n/a
18	POLR2A	chr19:39432171-39433917	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39424291..39427165-chr19:39431184..39433812,2	K562	blood:
2	chr19:39430639..39433501-chr19:39434198..39436514,3	K562	blood:
3	chr19:39419688..39423695-chr19:39432581..39436696,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269486	TF binding region
ENSG00000104835	Chromatin interaction
ENSG00000128626	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10410544	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10416055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425217	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10426382	1.00[JPT][hapmap]
rs10775533	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083489	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]
rs11668245	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462710	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610409	0.92[ASN][1000 genomes]
rs12972986	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979755	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12982957	0.86[EUR][1000 genomes]
rs17545254	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1808661	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1808662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865047	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865049	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2278412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs3136640	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs4801960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4801971	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802998	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4803006	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4803034	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs730078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7508411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508539	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9636109	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9749516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs575	SARS2	cis	multi-tissue	Pritchard
rs575	CTC-360G5.9	cis	Nerve Tibial	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422400-39434600	Weak transcription	Fetal Kidney	kidney
2	chr19:39422400-39435000	Weak transcription	Fetal Lung	lung
3	chr19:39422400-39435000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:39422400-39440600	Weak transcription	NHDF-Ad	bronchial
5	chr19:39422600-39435200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:39422600-39435200	Weak transcription	HSMM	muscle
7	chr19:39422600-39440200	Weak transcription	NH-A	brain
8	chr19:39422600-39440600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
10	chr19:39423200-39440800	Weak transcription	Fetal Heart	heart
11	chr19:39423400-39436800	Weak transcription	Aorta	Aorta
12	chr19:39423600-39433400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:39423600-39435000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:39423600-39440400	Weak transcription	Right Atrium	heart
15	chr19:39423600-39440600	Weak transcription	Gastric	stomach
16	chr19:39424000-39435200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:39424200-39435400	Weak transcription	NHLF	lung
18	chr19:39424400-39435000	Weak transcription	Adipose Nuclei	Adipose
19	chr19:39424400-39436800	Weak transcription	Brain Angular Gyrus	brain
20	chr19:39424400-39440000	Weak transcription	Fetal Brain Female	brain
21	chr19:39424600-39434400	Weak transcription	Fetal Intestine Large	intestine
22	chr19:39424600-39434600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:39424600-39434600	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:39424600-39436600	Weak transcription	Brain Anterior Caudate	brain
25	chr19:39424600-39440200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr19:39424600-39440200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:39424800-39440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:39424800-39440200	Weak transcription	Brain Substantia Nigra	brain
29	chr19:39425400-39436800	Weak transcription	Lung	lung
30	chr19:39425400-39440400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:39425600-39434400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:39425600-39434400	Weak transcription	Ovary	ovary
33	chr19:39425600-39434600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr19:39425600-39436800	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:39425600-39440200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:39425800-39433000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:39425800-39434600	Weak transcription	Osteobl	bone
38	chr19:39425800-39435000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:39425800-39435000	Weak transcription	Brain Germinal Matrix	brain
40	chr19:39425800-39435200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:39425800-39435200	Weak transcription	HepG2	liver
42	chr19:39425800-39435400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:39425800-39436400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:39425800-39437000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:39425800-39440200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:39425800-39440600	Weak transcription	Esophagus	oesophagus
47	chr19:39425800-39440600	Weak transcription	Left Ventricle	heart
48	chr19:39425800-39440600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr19:39425800-39440600	Weak transcription	Right Ventricle	heart
50	chr19:39425800-39440600	Weak transcription	NHEK	skin

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