Variant report

Variant	rs4613123
Chromosome Location	chr17:20929295-20929296
allele	C/T
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	chr17:20928679-20929832	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:20928664-20929402	GM12892	blood:	n/a	n/a
3	POLR2A	chr17:20928655-20929309	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr17:20928697-20929298	MCF-7	breast:	n/a	n/a
5	POLR2A	chr17:20929210-20929759	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:20928652-20929299	GM12892	blood:	n/a	n/a
7	POLR2A	chr17:20928852-20930025	A549	lung:	n/a	n/a
8	POLR2A	chr17:20928716-20929321	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20927260..20930029-chr17:20931065..20932995,3	K562	blood:
2	chr17:20919619..20922479-chr17:20927032..20929919,2	MCF-7	breast:

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

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1038107	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1038109	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1044410	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1044414	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1044420	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204330	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127815	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12103803	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12150138	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12600604	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1904230	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1993901	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009756	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2127094	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291036	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291037	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364327	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2364328	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2364329	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364330	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364331	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364332	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2364333	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3612	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816664	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3943299	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4462662	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985813	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985820	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985824	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985941	0.83[EUR][1000 genomes]
rs4985948	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4985949	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4985952	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4985953	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985954	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985955	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985957	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4985962	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985964	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985973	0.81[AMR][1000 genomes]
rs4985974	0.83[AMR][1000 genomes]
rs5005801	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587109	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587115	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71371043	0.89[ASN][1000 genomes]
rs7207724	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7207753	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7208779	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7213684	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7215369	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7216090	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7216449	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216786	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216978	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218112	0.84[EUR][1000 genomes]
rs7218443	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7221483	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7221757	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7223388	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7224746	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226229	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064435	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8076078	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8077998	0.85[ASN][1000 genomes]
rs899335	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs899336	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs899338	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs899341	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs899342	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs961004	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9797279	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9894624	0.90[ASN][1000 genomes]
rs9895047	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9896259	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9896301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9898265	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9902303	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs996065	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4613123	USP22	Cis_1M	lymphoblastoid	RTeQTL
rs4613123	USP22	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20900600-20932400	Strong transcription	Fetal Intestine Small	intestine
2	chr17:20900800-20932200	Strong transcription	Brain Germinal Matrix	brain
3	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
4	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
6	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
11	chr17:20902000-20935400	Strong transcription	Dnd41	blood
12	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
13	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:20902400-20931600	Strong transcription	HMEC	breast
15	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr17:20903400-20932000	Strong transcription	Liver	Liver
24	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:20905000-20933000	Strong transcription	Hela-S3	cervix
28	chr17:20905400-20931800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr17:20905800-20931600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:20906000-20931800	Strong transcription	HSMM	muscle
31	chr17:20906800-20932800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:20909200-20931800	Strong transcription	HUVEC	blood vessel
33	chr17:20909200-20932200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:20909400-20932400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr17:20909400-20932600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:20909600-20933200	Strong transcription	HepG2	liver
37	chr17:20923000-20933000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr17:20923200-20930600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr17:20924400-20931400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr17:20924400-20932600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr17:20925000-20931800	Strong transcription	Spleen	Spleen
43	chr17:20925000-20932000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr17:20925200-20933400	Weak transcription	Stomach Mucosa	stomach
45	chr17:20925400-20931800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr17:20925800-20930000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
47	chr17:20926000-20931600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr17:20926000-20931600	Strong transcription	Fetal Brain Female	brain
49	chr17:20926000-20931800	Strong transcription	NH-A	brain
50	chr17:20926000-20932200	Strong transcription	Primary B cells from cord blood	blood

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