Variant report

Variant	rs2281562
Chromosome Location	chr20:25273362-25273363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25272877-25273492	HL-60	blood:	n/a	n/a
2	POLR2A	chr20:25270778-25273679	A549	lung:	n/a	n/a
3	POLR2A	chr20:25273296-25273479	K562	blood:	n/a	n/a
4	POLR2A	chr20:25273062-25273466	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr20:25272818-25273675	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr20:25271036-25273641	K562	blood:	n/a	n/a
7	POLR2A	chr20:25273099-25273601	GM12878	blood:	n/a	n/a
8	POLR2A	chr20:25272780-25273533	GM12878	blood:	n/a	n/a
9	FOSL2	chr20:25273152-25273671	HepG2	liver:	n/a	n/a
10	POLR2A	chr20:25273240-25273440	GM12878	blood:	n/a	n/a
11	POLR2A	chr20:25273007-25273576	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr20:25273227-25273515	GM12878	blood:	n/a	n/a
13	POLR2A	chr20:25273023-25273497	A549	lung:	n/a	n/a
14	POLR2A	chr20:25271217-25273748	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr20:25272882-25273646	GM12878	blood:	n/a	n/a
16	CREB1	chr20:25272918-25273458	A549	lung:	n/a	n/a
17	POLR2A	chr20:25272763-25273673	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr20:25273058-25273709	PANC-1	pancreas:	n/a	n/a
19	POLR2A	chr20:25270585-25278923	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr20:25270332-25278907	A549	lung:	n/a	n/a
21	POLR2A	chr20:25272812-25273651	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr20:25270412-25273689	A549	lung:	n/a	n/a
23	POLR2A	chr20:25271510-25273557	HepG2	liver:	n/a	n/a
24	POLR2A	chr20:25273092-25273537	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr20:25273259-25273540	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr20:25273082-25273637	A549	lung:	n/a	n/a
27	POLR2A	chr20:25273101-25273571	HepG2	liver:	n/a	n/a
28	POLR2A	chr20:25273172-25273527	HCT-116	colon:	n/a	n/a
29	POLR2A	chr20:25273047-25273562	MCF-7	breast:	n/a	n/a
30	POLR2A	chr20:25272660-25273598	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25227365..25229517-chr20:25271304..25273431,2	MCF-7	breast:

No data

Variant related genes	Relation type
PYGB	TF binding region
ENSG00000100994	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11696666	0.85[ASN][1000 genomes]
rs12625157	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12625357	0.84[ASN][1000 genomes]
rs12625748	0.89[ASN][1000 genomes]
rs1962310	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2274890	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2281558	0.84[EUR][1000 genomes]
rs2281561	0.91[ASN][1000 genomes]
rs35084391	0.89[ASN][1000 genomes]
rs3764694	0.83[ASN][1000 genomes]
rs3787080	0.84[EUR][1000 genomes]
rs6115113	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs68053392	0.85[ASN][1000 genomes]
rs9305141	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv1798601	chr20:25250122-25305949	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
18	nsv912827	chr20:25271326-25288632	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2281562	PYGB	cis	occipital cortex	BrainEAC
rs2281562	PYGB	cis	brain	BrainEAC
rs2281562	PYGB	cis	cerebellar cortex	BrainEAC
rs2281562	PYGB	cis	temporal cortex	BrainEAC
rs2281562	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs2281562	PYGB	cis	substantia nigra	BrainEAC
rs2281562	PYGB	cis	putamen	BrainEAC
rs2281562	PYGB	cis	hippocampus	BrainEAC
rs2281562	PYGB	cis	thalamus	BrainEAC
rs2281562	PYGB	cis	Skin Sun Exposed Lower leg	GTEx
rs2281562	PYGB	cis	frontal cortex	BrainEAC

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:25235600-25291200	Weak transcription	Fetal Kidney	kidney
3	chr20:25247600-25277400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:25249000-25280200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr20:25249200-25274800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:25249200-25275000	Strong transcription	A549	lung
7	chr20:25249200-25285800	Strong transcription	Dnd41	blood
8	chr20:25249400-25274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr20:25249400-25274800	Strong transcription	Osteobl	bone
10	chr20:25249400-25276200	Strong transcription	Fetal Intestine Large	intestine
11	chr20:25249600-25273400	Strong transcription	NHEK	skin
12	chr20:25249600-25274400	Strong transcription	Lung	lung
13	chr20:25249600-25274600	Strong transcription	Primary T cells from cord blood	blood
14	chr20:25249600-25274600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr20:25249600-25274800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr20:25249600-25275000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr20:25249600-25275000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr20:25249600-25275000	Strong transcription	NHLF	lung
19	chr20:25249600-25275200	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr20:25249600-25279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr20:25249600-25279400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:25249600-25284800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr20:25249600-25285200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr20:25249800-25273400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:25249800-25273400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr20:25249800-25274000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr20:25249800-25274600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr20:25249800-25274600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:25249800-25275000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr20:25249800-25275200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr20:25249800-25275200	Strong transcription	Fetal Stomach	stomach
32	chr20:25249800-25276400	Strong transcription	Fetal Intestine Small	intestine
33	chr20:25249800-25284400	Strong transcription	Brain Germinal Matrix	brain
34	chr20:25250000-25274800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr20:25250000-25274800	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr20:25250000-25275800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:25250600-25276200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr20:25250800-25285000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr20:25251400-25275400	Strong transcription	Thymus	Thymus
40	chr20:25252200-25276400	Weak transcription	Hela-S3	cervix
41	chr20:25253800-25273800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr20:25254000-25276200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr20:25254200-25274600	Weak transcription	Psoas Muscle	Psoas
44	chr20:25254200-25275000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr20:25254400-25287800	Weak transcription	K562	blood
46	chr20:25255200-25273800	Strong transcription	Rectal Smooth Muscle	rectum
47	chr20:25255400-25273400	Strong transcription	Brain Anterior Caudate	brain
48	chr20:25255400-25274800	Strong transcription	Adipose Nuclei	Adipose
49	chr20:25255600-25279200	Strong transcription	Fetal Brain Female	brain
50	chr20:25255800-25290000	Weak transcription	Small Intestine	intestine

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