Variant report

Variant	rs2054464
Chromosome Location	chr17:20919720-20919721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20919466-20921064	GM12891	blood:	n/a	n/a
2	POLR2A	chr17:20919379-20921064	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr17:20919687-20919729	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr17:20919584-20919801	K562	blood:	n/a	n/a
5	POLR2A	chr17:20919573-20919761	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr17:20919453-20919728	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr17:20919515-20922766	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr17:20919400-20923329	HepG2	liver:	n/a	n/a
9	POLR2A	chr17:20919392-20921129	GM12892	blood:	n/a	n/a
10	POLR2A	chr17:20919601-20920193	MCF-7	breast:	n/a	n/a
11	POLR2A	chr17:20919318-20920199	GM12892	blood:	n/a	n/a
12	POLR2A	chr17:20919629-20919822	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr17:20919693-20920009	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr17:20919418-20921060	GM12892	blood:	n/a	n/a
15	POLR2A	chr17:20919543-20925272	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr17:20917991-20921614	A549	lung:	n/a	n/a
17	POLR2A	chr17:20917596-20921783	K562	blood:	n/a	n/a
18	POLR2A	chr17:20919461-20919846	K562	blood:	n/a	n/a
19	POLR2A	chr17:20918057-20921119	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:20918951-20919785	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:20918559..20920846-chr17:20922682..20924740,2	K562	blood:
2	chr17:20916181..20917774-chr17:20918332..20921119,2	MCF-7	breast:
3	chr17:20918559..20920531-chr17:20920767..20924740,3	K562	blood:
4	chr17:20916495..20920338-chr17:20933999..20937587,3	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHRS7B-7	chr17:20919461-20919862	NONHSAT052155
2	lnc-DHRS7B-7	chr17:20919473-20919862	l_1417_chr17:20919472-20934581_brain

No data

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

Extended variants
information (count: 45 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1045162	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1127814	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12051606	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12600703	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12601292	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12602058	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12943067	0.84[ASN][1000 genomes]
rs12946114	0.88[ASN][1000 genomes]
rs1542552	0.93[AMR][1000 genomes]
rs17770614	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2127095	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291034	0.95[ASN][1000 genomes]
rs2364326	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2886105	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4445951	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4985811	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4985814	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985815	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985816	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985959	0.88[ASN][1000 genomes]
rs4985963	0.89[ASN][1000 genomes]
rs4985966	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985967	0.84[ASN][1000 genomes]
rs4985968	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985969	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985970	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985971	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4985975	0.89[AMR][1000 genomes]
rs56323013	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58235085	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59543297	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59713572	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6587111	0.86[ASN][1000 genomes]
rs6587114	0.83[ASN][1000 genomes]
rs6618	0.88[ASN][1000 genomes]
rs719093	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209129	0.91[ASN][1000 genomes]
rs7216921	0.86[ASN][1000 genomes]
rs880653	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs899337	0.88[AMR][1000 genomes]
rs899340	0.89[ASN][1000 genomes]
rs9911289	0.88[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2054464	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs2054464	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs2054464	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2054464	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs2054464	RP11-344E13.3	cis	Artery Tibial	GTEx
rs2054464	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs2054464	RP11-344E13.3	cis	Stomach	GTEx
rs2054464	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs2054464	RP11-344E13.3	cis	lung	GTEx
rs2054464	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs2054464	RP11-344E13.3	cis	Whole Blood	GTEx
rs2054464	RP11-344E13.3	cis	Thyroid	GTEx

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	chr17:20901400-20925200	Strong transcription	Fetal Lung	lung
6	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
7	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
9	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr17:20902000-20925200	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
15	chr17:20902000-20935400	Strong transcription	Dnd41	blood
16	chr17:20902200-20925200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
18	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr17:20902400-20927000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr17:20902400-20931600	Strong transcription	HMEC	breast
21	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr17:20902600-20924200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:20902600-20925400	Strong transcription	NHEK	skin
26	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr17:20902800-20923600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr17:20902800-20925200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr17:20902800-20925200	Strong transcription	Colonic Mucosa	Colon
33	chr17:20903200-20925200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr17:20903400-20932000	Strong transcription	Liver	Liver
36	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:20903800-20924000	Strong transcription	Lung	lung
39	chr17:20903800-20925000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
40	chr17:20904000-20928200	Strong transcription	A549	lung
41	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr17:20904200-20926600	Strong transcription	Primary T cells from cord blood	blood
43	chr17:20904600-20925200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr17:20904600-20925200	Strong transcription	NH-A	brain
45	chr17:20904800-20924800	Strong transcription	Fetal Kidney	kidney
46	chr17:20905000-20923800	Strong transcription	Pancreas	Pancrea
47	chr17:20905000-20925200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:20905000-20933000	Strong transcription	Hela-S3	cervix
49	chr17:20905200-20923400	Strong transcription	Aorta	Aorta
50	chr17:20905200-20926600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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