Variant report

Variant	rs1904230
Chromosome Location	chr17:20944220-20944221
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20943721..20945424-chr17:21006912..21008982,2	K562	blood:
2	chr17:20943445..20945736-chr17:21186305..21189168,3	K562	blood:
3	chr17:20923323..20925346-chr17:20944193..20946472,2	MCF-7	breast:
4	chr17:20923120..20926842-chr17:20942462..20946048,5	K562	blood:
5	chr17:20922289..20926435-chr17:20942892..20947042,7	MCF-7	breast:
6	chr17:20923333..20926205-chr17:20942462..20944595,2	K562	blood:
7	chr17:20942946..20947008-chr17:21027887..21030893,3	K562	blood:

Variant related genes	Relation type
ENSG00000109016	Chromatin interaction
ENSG00000124422	Chromatin interaction
ENSG00000034152	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1038107	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1038109	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1044410	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1044414	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1044420	0.82[ASN][1000 genomes]
rs11204330	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1127815	0.82[AMR][1000 genomes]
rs12103803	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12150138	0.83[ASN][1000 genomes]
rs1993901	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2009756	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2127094	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2291036	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2291037	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2364327	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2364328	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2364329	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2364330	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2364331	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2364332	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2364333	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3612	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3816664	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3943299	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4462662	0.83[ASN][1000 genomes]
rs4613123	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4985813	0.85[AMR][1000 genomes]
rs4985820	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4985824	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4985953	0.80[AMR][1000 genomes]
rs4985955	0.80[AMR][1000 genomes]
rs4985957	0.86[AMR][1000 genomes]
rs4985962	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4985964	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5005801	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6587109	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6587115	0.83[ASN][1000 genomes]
rs71371043	0.83[ASN][1000 genomes]
rs7207724	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7207753	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7208779	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7213684	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7215369	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7216449	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7216786	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7216978	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7218443	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7219244	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7221483	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7221757	0.86[AMR][1000 genomes]
rs7224746	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7226229	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8064435	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs899335	0.80[AMR][1000 genomes]
rs899336	0.80[AMR][1000 genomes]
rs899338	0.81[AMR][1000 genomes]
rs899341	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9797279	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9894624	0.82[ASN][1000 genomes]
rs9896259	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9896301	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9898265	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9902303	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs996065	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv827918	chr17:20941127-20951156	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv827921	chr17:20943553-20951115	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1904230	USP22	cis	Whole Blood	GTEx
rs1904230	USP22	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20942400-20944800	Enhancers	Spleen	Spleen
2	chr17:20942600-20945000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:20942800-20944600	Flanking Active TSS	HepG2	liver
4	chr17:20942800-20944800	Enhancers	Stomach Mucosa	stomach
5	chr17:20942800-20945600	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr17:20943000-20944800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:20943000-20947200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr17:20943200-20944400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:20943200-20944400	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr17:20943200-20944800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:20943200-20945200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:20943200-20947200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr17:20943200-20947200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr17:20943200-20947200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr17:20943400-20944400	Active TSS	K562	blood
16	chr17:20943400-20944600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:20943400-20945800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:20943400-20947200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:20943400-20947200	Active TSS	Aorta	Aorta
20	chr17:20943400-20947200	Active TSS	Brain Angular Gyrus	brain
21	chr17:20943400-20947200	Active TSS	Ovary	ovary
22	chr17:20943400-20947200	Active TSS	GM12878-XiMat	blood
23	chr17:20943400-20947200	Active TSS	NHDF-Ad	bronchial
24	chr17:20943400-20947400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr17:20943400-20947400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr17:20943600-20944400	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr17:20943600-20944400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr17:20943600-20944400	Flanking Active TSS	Fetal Thymus	thymus
29	chr17:20943600-20944400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr17:20943600-20944400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr17:20943600-20944600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr17:20943600-20944600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr17:20943600-20944600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr17:20943600-20944600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:20943600-20944600	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr17:20943600-20944600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr17:20943600-20945000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr17:20943600-20945400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr17:20943600-20947000	Active TSS	Colonic Mucosa	Colon
40	chr17:20943600-20947200	Active TSS	HSMMtube	muscle
41	chr17:20943600-20947600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr17:20943600-20947800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr17:20943600-20947800	Active TSS	H9 Cell Line	embryonic stem cell
44	chr17:20943800-20944400	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr17:20943800-20944400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr17:20943800-20944600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr17:20943800-20944600	Flanking Active TSS	Liver	Liver
48	chr17:20943800-20944600	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr17:20943800-20945000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:20943800-20945200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood

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