Variant report

Variant	rs59543297
Chromosome Location	chr17:20928768-20928769
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:20928679-20929832	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:20928664-20929402	GM12892	blood:	n/a	n/a
3	CTCF	chr17:20928760-20928910	AG04449	skin:	n/a	n/a
4	MYC	chr17:20928734-20929070	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr17:20928655-20929309	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr17:20928489-20929277	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr17:20928749-20928927	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:20928697-20929298	MCF-7	breast:	n/a	n/a
9	POLR2A	chr17:20928652-20929299	GM12892	blood:	n/a	n/a
10	POLR2A	chr17:20927079-20929169	K562	blood:	n/a	n/a
11	POLR2A	chr17:20928695-20929043	GM12891	blood:	n/a	n/a
12	POLR2A	chr17:20928716-20929321	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20927260..20930029-chr17:20931065..20932995,3	K562	blood:
2	chr17:20919619..20922479-chr17:20927032..20929919,2	MCF-7	breast:

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	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1127814	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12051606	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12600703	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12601292	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12602058	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12943067	0.83[ASN][1000 genomes]
rs12946114	0.89[ASN][1000 genomes]
rs1542552	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17770614	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2054464	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2127095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291034	0.93[ASN][1000 genomes]
rs2364326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2886105	0.86[AMR][1000 genomes]
rs4445951	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985811	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4985814	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985815	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985816	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985959	0.86[ASN][1000 genomes]
rs4985963	0.91[ASN][1000 genomes]
rs4985966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985967	0.86[ASN][1000 genomes]
rs4985968	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985970	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985971	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985975	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56323013	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58235085	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59713572	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6587111	0.88[ASN][1000 genomes]
rs6587114	0.82[ASN][1000 genomes]
rs6618	0.86[ASN][1000 genomes]
rs719093	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7209129	0.89[ASN][1000 genomes]
rs7216921	0.85[ASN][1000 genomes]
rs880653	0.86[AMR][1000 genomes]
rs899337	0.87[AMR][1000 genomes]
rs899340	0.88[ASN][1000 genomes]
rs9911289	0.86[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
rs59543297	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs59543297	RP11-344E13.3	cis	Stomach	GTEx
rs59543297	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs59543297	RP11-344E13.3	cis	Thyroid	GTEx
rs59543297	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs59543297	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs59543297	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs59543297	RP11-344E13.3	cis	Artery Tibial	GTEx
rs59543297	RP11-344E13.3	cis	lung	GTEx
rs59543297	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs59543297	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs59543297	RP11-344E13.3	cis	Whole Blood	GTEx

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	chr17:20900800-20932200	Strong transcription	Brain Germinal Matrix	brain
3	chr17:20901400-20932600	Strong transcription	Thymus	Thymus
4	chr17:20901400-20937000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr17:20901800-20929400	Strong transcription	GM12878-XiMat	blood
6	chr17:20901800-20932000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr17:20901800-20932000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:20901800-20932400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr17:20901800-20936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:20902000-20932600	Strong transcription	Fetal Intestine Large	intestine
11	chr17:20902000-20935400	Strong transcription	Dnd41	blood
12	chr17:20902200-20932400	Strong transcription	Fetal Thymus	thymus
13	chr17:20902200-20932600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:20902400-20931600	Strong transcription	HMEC	breast
15	chr17:20902400-20932200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr17:20902400-20932200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr17:20902400-20932600	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr17:20902600-20932000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:20902600-20932200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr17:20902600-20932400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr17:20902600-20932800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:20903200-20932000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr17:20903400-20932000	Strong transcription	Liver	Liver
24	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:20903600-20938400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr17:20904000-20931600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:20905000-20933000	Strong transcription	Hela-S3	cervix
28	chr17:20905400-20931800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr17:20905800-20931600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:20906000-20931800	Strong transcription	HSMM	muscle
31	chr17:20906800-20932800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:20909200-20931800	Strong transcription	HUVEC	blood vessel
33	chr17:20909200-20932200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr17:20909400-20932400	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr17:20909400-20932600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:20909600-20933200	Strong transcription	HepG2	liver
37	chr17:20912000-20928800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr17:20923000-20933000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr17:20923200-20930600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr17:20924400-20931400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr17:20924400-20932600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr17:20925000-20929000	Weak transcription	Fetal Heart	heart
44	chr17:20925000-20931800	Strong transcription	Spleen	Spleen
45	chr17:20925000-20932000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:20925200-20933400	Weak transcription	Stomach Mucosa	stomach
47	chr17:20925400-20931800	Strong transcription	Fetal Muscle Trunk	muscle
48	chr17:20925800-20930000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr17:20926000-20929000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:20926000-20931600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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