Variant report

Variant	rs719094
Chromosome Location	chr17:20916797-20916798
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20915675-20916902	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:20915510-20916841	GM12878	blood:	n/a	n/a
3	POLR2A	chr17:20916500-20916812	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:20910057-20917039	K562	blood:	n/a	n/a
5	POLR2A	chr17:20913999-20917147	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr17:20916658-20917020	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr17:20916489-20916807	K562	blood:	n/a	n/a
8	POLR2A	chr17:20916605-20916876	K562	blood:	n/a	n/a
9	POLR2A	chr17:20916762-20916812	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:20916047..20919088-chr17:20919633..20922601,3	K562	blood:
2	chr17:20910306..20913499-chr17:20915103..20918018,3	MCF-7	breast:
3	chr17:20916495..20920338-chr17:20933999..20937587,3	K562	blood:
4	chr17:20916181..20917774-chr17:20918332..20921119,2	MCF-7	breast:
5	chr17:20916459..20918051-chr17:20921682..20924562,2	K562	blood:

No data

Variant related genes	Relation type
USP22	TF binding region
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10153263	0.96[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10512422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11541314	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11650653	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869201	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11869217	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11869959	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12450389	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12452171	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12937950	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947514	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16962364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1871275	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28663143	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2886049	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34354508	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35022634	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4381653	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4427861	0.90[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4985942	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985945	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55633111	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57522885	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587107	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587113	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587116	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66487709	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66516868	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73303698	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072149	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8080321	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs984007	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9893047	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9895277	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9895618	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9896853	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9907786	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9909279	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9914758	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9914916	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs719094	USP22	cis	intralobular white matter	BrainEAC
rs719094	USP22	cis	thalamus	BrainEAC
rs719094	ALDH3A1	cis	cerebellum	SCAN
rs719094	RP11-381P6.1	cis	Muscle Skeletal	GTEx
rs719094	SMCR7	cis	cerebellum	SCAN
rs719094	USP22	cis	occipital cortex	BrainEAC
rs719094	USP22	cis	brain	BrainEAC
rs719094	USP22	cis	lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20900200-20924000	Strong transcription	Fetal Stomach	stomach
2	chr17:20900600-20932400	Strong transcription	Fetal Intestine Small	intestine
3	chr17:20900800-20925600	Strong transcription	Fetal Brain Female	brain
4	chr17:20900800-20932200	Strong transcription	Brain Germinal Matrix	brain
5	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
6	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
7	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
9	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:20902000-20925200	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
15	chr17:20902000-20935400	Strong transcription	Dnd41	blood
16	chr17:20902200-20918600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr17:20902200-20925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
19	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr17:20902400-20927000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr17:20902400-20931600	Strong transcription	HMEC	breast
22	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr17:20902600-20924200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr17:20902600-20925400	Strong transcription	NHEK	skin
27	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr17:20902800-20923600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:20902800-20925200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr17:20902800-20925200	Strong transcription	Colonic Mucosa	Colon
34	chr17:20903200-20917000	Strong transcription	Esophagus	oesophagus
35	chr17:20903200-20925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr17:20903400-20932000	Strong transcription	Liver	Liver
38	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr17:20903800-20924000	Strong transcription	Lung	lung
41	chr17:20903800-20925000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr17:20904000-20928200	Strong transcription	A549	lung
43	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr17:20904200-20926600	Strong transcription	Primary T cells from cord blood	blood
45	chr17:20904600-20925200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr17:20904600-20925200	Strong transcription	NH-A	brain
47	chr17:20904800-20924800	Strong transcription	Fetal Kidney	kidney
48	chr17:20905000-20923800	Strong transcription	Pancreas	Pancrea
49	chr17:20905000-20925200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:20905000-20933000	Strong transcription	Hela-S3	cervix

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