Variant report

Variant	rs2291037
Chromosome Location	chr17:20924523-20924524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20923956-20924631	GM12891	blood:	n/a	n/a
2	POLR2A	chr17:20923863-20924733	GM12891	blood:	n/a	n/a
3	POLR2A	chr17:20924420-20924952	GM12891	blood:	n/a	n/a
4	POLR2A	chr17:20924254-20924573	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr17:20924484-20924524	HepG2	liver:	n/a	n/a
6	POLR2A	chr17:20923637-20925075	HepG2	liver:	n/a	n/a
7	POLR2A	chr17:20922041-20925194	K562	blood:	n/a	n/a
8	POLR2A	chr17:20923462-20924884	GM12892	blood:	n/a	n/a
9	POLR2A	chr17:20922111-20925115	A549	lung:	n/a	n/a
10	POLR2A	chr17:20919543-20925272	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr17:20923553-20925128	GM12892	blood:	n/a	n/a
12	POLR2A	chr17:20923523-20924833	GM12878	blood:	n/a	n/a
13	POLR2A	chr17:20924340-20925318	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:20923120..20926842-chr17:20942462..20946048,5	K562	blood:
2	chr17:20923323..20925346-chr17:20944193..20946472,2	MCF-7	breast:
3	chr17:20922289..20926435-chr17:20942892..20947042,7	MCF-7	breast:

No data

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

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1038107	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1038109	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1044410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1044414	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1044420	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204330	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1127815	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12103803	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150138	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1904230	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1993901	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009756	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127094	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291036	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364327	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364328	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2364329	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364330	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364331	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364332	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2364333	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3612	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816664	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3943299	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4462662	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4613123	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4985813	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4985820	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985824	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985935	0.86[JPT][hapmap]
rs4985941	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs4985948	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs4985949	0.83[AMR][1000 genomes]
rs4985952	0.83[AMR][1000 genomes]
rs4985953	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985954	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985955	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4985957	0.85[AMR][1000 genomes]
rs4985962	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985964	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985974	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs5005801	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587109	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587115	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71371043	0.89[ASN][1000 genomes]
rs7207724	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7207753	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7208779	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7211094	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap]
rs7213684	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7215369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7216090	0.84[ASN][1000 genomes]
rs7216449	0.95[CEU][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7216786	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7216978	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7218112	0.85[CEU][hapmap];0.91[CHB][hapmap]
rs7218443	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7219244	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7221483	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7221757	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7223388	0.90[CEU][hapmap];0.95[JPT][hapmap]
rs7224746	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7226229	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8064435	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8071311	0.86[JPT][hapmap]
rs8075790	0.91[JPT][hapmap]
rs8077998	0.84[ASN][1000 genomes]
rs880652	0.91[JPT][hapmap]
rs899335	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs899336	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs899338	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs899341	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs899342	0.90[CEU][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs9797279	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9894624	0.89[ASN][1000 genomes]
rs9895047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9896259	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9896301	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9898265	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9902303	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs996065	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2291037	USP22	Cis_1M	lymphoblastoid	RTeQTL
rs2291037	FAM27L	cis	cerebellum	SCAN
rs2291037	SLC5A10	cis	parietal	SCAN

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	chr17:20900800-20925600	Strong transcription	Fetal Brain Female	brain
3	chr17:20900800-20932200	Strong transcription	Brain Germinal Matrix	brain
4	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
5	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
6	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
8	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:20902000-20925200	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
14	chr17:20902000-20935400	Strong transcription	Dnd41	blood
15	chr17:20902200-20925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
17	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr17:20902400-20927000	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr17:20902400-20931600	Strong transcription	HMEC	breast
20	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr17:20902600-20925400	Strong transcription	NHEK	skin
24	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr17:20902800-20925200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:20902800-20925200	Strong transcription	Colonic Mucosa	Colon
30	chr17:20903200-20925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr17:20903400-20932000	Strong transcription	Liver	Liver
33	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr17:20903800-20925000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
36	chr17:20904000-20928200	Strong transcription	A549	lung
37	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr17:20904200-20926600	Strong transcription	Primary T cells from cord blood	blood
39	chr17:20904600-20925200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr17:20904600-20925200	Strong transcription	NH-A	brain
41	chr17:20904800-20924800	Strong transcription	Fetal Kidney	kidney
42	chr17:20905000-20925200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:20905000-20933000	Strong transcription	Hela-S3	cervix
44	chr17:20905200-20926600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr17:20905400-20925200	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr17:20905400-20931800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr17:20905600-20924800	Strong transcription	K562	blood
48	chr17:20905600-20925000	Strong transcription	NHDF-Ad	bronchial
49	chr17:20905600-20925600	Strong transcription	Duodenum Mucosa	Duodenum
50	chr17:20905600-20926800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links