Variant report

Variant	rs16962375
Chromosome Location	chr17:20910984-20910985
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20910904-20911302	GM12892	blood:	n/a	n/a
2	POLR2A	chr17:20910962-20911454	K562	blood:	n/a	n/a
3	POLR2A	chr17:20910446-20911427	GM12878	blood:	n/a	n/a
4	POLR2A	chr17:20910756-20911054	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:20910160-20911074	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr17:20910718-20911467	K562	blood:	n/a	n/a
7	POLR2A	chr17:20910880-20910994	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:20910057-20917039	K562	blood:	n/a	n/a
9	POLR2A	chr17:20910620-20911314	GM12892	blood:	n/a	n/a
10	POLR2A	chr17:20909796-20911796	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr17:20910165-20912103	HepG2	liver:	n/a	n/a
12	POLR2A	chr17:20909929-20912236	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr17:20910921-20911376	GM12891	blood:	n/a	n/a
14	POLR2A	chr17:20910007-20911446	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:20909787..20912757-chr17:20913311..20915722,3	K562	blood:
2	chr17:20906821..20909810-chr17:20910174..20912861,2	MCF-7	breast:
3	chr17:20910306..20913499-chr17:20915103..20918018,3	MCF-7	breast:
4	chr17:20907867..20912757-chr17:20913311..20916594,7	K562	blood:

No data

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

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1045215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10512423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204325	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes]
rs11204327	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11204329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204331	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11541311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11650623	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs11651078	0.85[AMR][1000 genomes]
rs11651500	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11652224	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11653213	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11653504	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11654801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11655512	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes]
rs11655985	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11656525	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11656662	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11656837	0.87[ASN][1000 genomes]
rs11656874	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11657155	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11658178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11658389	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11658671	0.91[ASN][1000 genomes]
rs11658722	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11658742	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs11658791	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11869271	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11870338	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs16942330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16962469	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2009757	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785544	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3891644	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985938	0.82[AMR][1000 genomes]
rs4985939	0.82[AMR][1000 genomes]
rs62055504	0.82[AMR][1000 genomes]
rs62055511	0.82[AMR][1000 genomes]
rs62056764	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62056765	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62056768	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62056770	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62056771	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62056832	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62058987	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62058990	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62058991	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62058993	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62059000	0.85[ASN][1000 genomes]
rs62059001	0.81[ASN][1000 genomes]
rs716959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7217797	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes]
rs7218520	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8079468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8080233	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9325900	0.84[ASN][1000 genomes]
rs9905095	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs9914432	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs9972887	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

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	chr17:20901400-20912200	Strong transcription	Primary B cells from cord blood	blood
6	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
7	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
8	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
10	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:20902000-20925200	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
16	chr17:20902000-20935400	Strong transcription	Dnd41	blood
17	chr17:20902200-20918600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr17:20902200-20925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
20	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:20902400-20927000	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr17:20902400-20931600	Strong transcription	HMEC	breast
23	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr17:20902600-20924200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:20902600-20925400	Strong transcription	NHEK	skin
28	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:20902800-20923600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr17:20902800-20925200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr17:20902800-20925200	Strong transcription	Colonic Mucosa	Colon
35	chr17:20903000-20911000	Genic enhancers	Brain Cingulate Gyrus	brain
36	chr17:20903200-20917000	Strong transcription	Esophagus	oesophagus
37	chr17:20903200-20925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr17:20903400-20932000	Strong transcription	Liver	Liver
40	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:20903800-20924000	Strong transcription	Lung	lung
43	chr17:20903800-20925000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr17:20904000-20928200	Strong transcription	A549	lung
45	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr17:20904200-20926600	Strong transcription	Primary T cells from cord blood	blood
47	chr17:20904600-20925200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr17:20904600-20925200	Strong transcription	NH-A	brain
49	chr17:20904800-20911000	Genic enhancers	Brain Substantia Nigra	brain
50	chr17:20904800-20912800	Strong transcription	Primary hematopoietic stem cells	blood

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