Variant report

Variant	rs62262683
Chromosome Location	chr3:49723147-49723148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49722479-49723496	GM12892	blood:	n/a	n/a
2	RXRA	chr3:49722714-49723470	HepG2	liver:	n/a	chr3:49722948-49722957
3	POLR2A	chr3:49722689-49723262	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:49721456-49727648	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:49717503-49727239	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49720128-49724935	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49722602-49725401	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:49722533-49723398	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:49722955-49723358	K562	blood:	n/a	n/a
10	POLR2A	chr3:49716580-49724829	HepG2	liver:	n/a	n/a
11	JUND	chr3:49721387-49723325	HepG2	liver:	n/a	n/a
12	GABPA	chr3:49723078-49723403	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:49721295-49723518	GM12892	blood:	n/a	n/a
14	POLR2A	chr3:49722993-49723324	PANC-1	pancreas:	n/a	n/a
15	ZBTB33	chr3:49723110-49723456	K562	blood:	n/a	n/a
16	POLR2A	chr3:49723134-49724607	A549	lung:	n/a	n/a
17	POLR2A	chr3:49721601-49723433	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:49716518-49723590	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:49722846-49723207	HL-60	blood:	n/a	n/a
20	FOSL2	chr3:49721509-49723262	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:49722926-49723378	H1-hESC	embryonic stem cell:	n/a	n/a
22	HEY1	chr3:49718256-49727412	HepG2	liver:	n/a	n/a
23	POU2F2	chr3:49722143-49723345	GM12878	blood:	n/a	n/a
24	POLR2A	chr3:49722625-49725083	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr3:49721241-49724664	GM12892	blood:	n/a	n/a
26	POLR2A	chr3:49722714-49723323	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:49723077-49723542	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr3:49723123-49723379	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr3:49721694-49724714	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:49722792-49723573	SK-N-MC	brain:	n/a	n/a
31	POLR2A	chr3:49721676-49723718	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49715211..49719699-chr3:49722366..49724649,4	K562	blood:
2	chr3:49722536..49724153-chr3:49724898..49727146,2	MCF-7	breast:
3	chr3:49710552..49715225-chr3:49718907..49727364,14	MCF-7	breast:
4	chr3:49711727..49717769-chr3:49722772..49726950,7	K562	blood:
5	chr1:16964923..16974624-chr3:49722461..49732046,16	K562	blood:

No data

Variant related genes	Relation type
RNF123	TF binding region
MST1	TF binding region
ENSG00000259970	TF binding region
ENSG00000186301	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000173531	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000215908	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs41290716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259945	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62260717	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62261251	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262670	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62262676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv11877	chr3:49721171-49727086	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	nsv471425	chr3:49721381-49726196	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv482080	chr3:49721381-49726196	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv822077	chr3:49721400-49734526	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	esv1825475	chr3:49722732-49734243	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49712200-49723800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49712800-49723600	Weak transcription	Right Atrium	heart
3	chr3:49712800-49726200	Weak transcription	Small Intestine	intestine
4	chr3:49713000-49723200	Weak transcription	Stomach Mucosa	stomach
5	chr3:49713000-49723400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:49713000-49723800	Weak transcription	Fetal Heart	heart
7	chr3:49714000-49723200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:49714200-49723200	Strong transcription	Dnd41	blood
9	chr3:49714600-49723800	Strong transcription	Liver	Liver
10	chr3:49717400-49723800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:49717600-49723800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:49719000-49726200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:49719800-49723200	Weak transcription	Psoas Muscle	Psoas
14	chr3:49719800-49723600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:49719800-49724400	Weak transcription	NHDF-Ad	bronchial
16	chr3:49720200-49723800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:49720400-49723200	Weak transcription	NH-A	brain
18	chr3:49720600-49726200	Weak transcription	A549	lung
19	chr3:49721000-49726200	Weak transcription	HSMM	muscle
20	chr3:49721200-49723200	Weak transcription	Right Ventricle	heart
21	chr3:49721200-49723400	Genic enhancers	HepG2	liver
22	chr3:49721200-49723600	Weak transcription	Primary B cells from cord blood	blood
23	chr3:49721400-49723200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:49721400-49723200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:49721400-49723200	Weak transcription	Left Ventricle	heart
26	chr3:49721400-49723200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:49721400-49723800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:49721400-49723800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:49721400-49724400	Weak transcription	Brain Angular Gyrus	brain
30	chr3:49721400-49725800	Weak transcription	Hela-S3	cervix
31	chr3:49721400-49725800	Weak transcription	K562	blood
32	chr3:49721400-49726400	Weak transcription	Aorta	Aorta
33	chr3:49721600-49723200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:49721600-49723200	Weak transcription	Brain Substantia Nigra	brain
35	chr3:49721600-49723200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:49721600-49723200	Weak transcription	NHLF	lung
37	chr3:49721600-49723800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:49721600-49723800	Weak transcription	GM12878-XiMat	blood
39	chr3:49721600-49726200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:49721800-49723800	Weak transcription	Primary T cells from cord blood	blood
41	chr3:49722000-49723200	Weak transcription	Colonic Mucosa	Colon
42	chr3:49722000-49723200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:49722000-49723200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:49722000-49723200	Weak transcription	HMEC	breast
45	chr3:49722000-49723800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:49722000-49724600	Weak transcription	Brain Anterior Caudate	brain
47	chr3:49722000-49724600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:49722200-49723200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:49722200-49723200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:49722200-49723200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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