Variant report

Variant	rs7208779
Chromosome Location	chr17:20940347-20940348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20932232..20934940-chr17:20938795..20941578,2	MCF-7	breast:
2	chr17:20934273..20942906-chr17:20943761..20949798,22	MCF-7	breast:
3	chr17:20936833..20939628-chr17:20939684..20941380,2	MCF-7	breast:

Variant related genes	Relation type
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];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1038109	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1044410	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1044414	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1044420	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204330	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1127815	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12103803	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150138	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12600604	0.83[EUR][1000 genomes]
rs1904230	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1993901	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009756	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2127094	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291036	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291037	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364327	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364328	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364329	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364330	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364331	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364332	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2364333	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3612	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816664	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3943299	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4462662	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4613123	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985813	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985820	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985824	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985941	0.81[EUR][1000 genomes]
rs4985948	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4985949	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4985952	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4985953	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985954	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985955	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985957	0.86[AMR][1000 genomes]
rs4985962	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985964	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587109	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6587115	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71371043	0.90[ASN][1000 genomes]
rs7207724	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7207753	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7213684	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215369	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216090	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7216449	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216786	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216978	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7218112	0.83[EUR][1000 genomes]
rs7218443	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7219244	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7221483	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7221757	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7223388	0.80[AMR][1000 genomes]
rs7224746	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7226229	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8064435	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8076078	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8077998	0.85[ASN][1000 genomes]
rs899335	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899336	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899338	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs899341	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs899342	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs961004	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9797279	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9894624	0.88[ASN][1000 genomes]
rs9895047	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9896259	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9896301	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9898265	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9902303	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs996065	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7208779	USP22	Cis_1M	lymphoblastoid	RTeQTL
rs7208779	USP22	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:20932200-20941400	Genic enhancers	A549	lung
3	chr17:20932600-20940400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:20932800-20941800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:20934000-20942800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:20934000-20943200	Weak transcription	Esophagus	oesophagus
7	chr17:20935000-20940600	Enhancers	Left Ventricle	heart
8	chr17:20935000-20941000	Enhancers	Right Ventricle	heart
9	chr17:20935200-20943800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr17:20935600-20942200	Enhancers	Fetal Brain Male	brain
11	chr17:20935800-20940600	Enhancers	Fetal Heart	heart
12	chr17:20936200-20941600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:20936400-20940800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr17:20936600-20941000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr17:20936600-20941200	Genic enhancers	HUVEC	blood vessel
16	chr17:20936800-20941800	Genic enhancers	NHEK	skin
17	chr17:20936800-20942000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:20936800-20943800	Enhancers	Liver	Liver
19	chr17:20937400-20941200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr17:20937400-20941200	Enhancers	Colonic Mucosa	Colon
21	chr17:20937600-20941400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr17:20937600-20942000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
23	chr17:20937800-20940600	Enhancers	H9 Cell Line	embryonic stem cell
24	chr17:20938000-20940400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr17:20938000-20941600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:20938000-20941800	Enhancers	Colon Smooth Muscle	Colon
27	chr17:20938200-20940400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:20938200-20940600	Enhancers	Primary B cells from peripheral blood	blood
29	chr17:20938200-20941200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr17:20938200-20943600	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr17:20938400-20940600	Enhancers	Brain Angular Gyrus	brain
32	chr17:20938400-20940800	Enhancers	Brain Hippocampus Middle	brain
33	chr17:20938400-20940800	Enhancers	HSMMtube	muscle
34	chr17:20938400-20941200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr17:20938400-20941400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr17:20938400-20941400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr17:20938400-20941800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr17:20938400-20943200	Weak transcription	Lung	lung
39	chr17:20938400-20944000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr17:20938600-20940600	Enhancers	Rectal Smooth Muscle	rectum
41	chr17:20938800-20940400	Weak transcription	Aorta	Aorta
42	chr17:20938800-20940600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr17:20938800-20941400	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr17:20938800-20941400	Enhancers	NH-A	brain
45	chr17:20938800-20941800	Genic enhancers	Rectal Mucosa Donor 29	rectum
46	chr17:20939000-20940400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr17:20939000-20940400	Weak transcription	Stomach Mucosa	stomach
48	chr17:20939000-20943200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr17:20939200-20942200	Genic enhancers	Primary hematopoietic stem cells	blood
50	chr17:20939200-20942800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links