Variant report

Variant	rs11709284
Chromosome Location	chr3:52559705-52559706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52557221-52564466	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:52558355-52560710	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:52559464-52560665	NB4	blood:	n/a	n/a
4	POLR2A	chr3:52556703-52560542	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:52557107-52565043	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:52559237-52560630	K562	blood:	n/a	n/a
7	POLR2A	chr3:52557044-52564804	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:52489123..52491255-chr3:52558992..52560564,2	MCF-7	breast:
2	chr3:52551111..52554473-chr3:52556873..52560591,3	MCF-7	breast:
3	chr3:52559482..52561203-chr3:52562436..52565441,3	MCF-7	breast:
4	chr3:52553170..52556656-chr3:52557821..52561228,3	MCF-7	breast:

No data

Variant related genes	Relation type
NT5DC2	TF binding region
ENSG00000010327	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1010553	0.84[EUR][1000 genomes]
rs1010554	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130306	0.81[EUR][1000 genomes]
rs1133415	0.93[ASN][1000 genomes]
rs11711421	0.85[ASN][1000 genomes]
rs12489732	0.92[ASN][1000 genomes]
rs12489828	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13059862	0.90[ASN][1000 genomes]
rs13060048	0.90[ASN][1000 genomes]
rs13063160	0.90[ASN][1000 genomes]
rs13076398	0.92[ASN][1000 genomes]
rs13081028	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13303	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13621	0.93[ASN][1000 genomes]
rs1570	0.91[ASN][1000 genomes]
rs17052256	0.91[ASN][1000 genomes]
rs17052259	0.91[ASN][1000 genomes]
rs1821879	0.88[ASN][1000 genomes]
rs1961958	0.87[ASN][1000 genomes]
rs1961959	0.89[ASN][1000 genomes]
rs2251219	0.90[ASN][1000 genomes]
rs2276824	0.80[ASN][1000 genomes]
rs2289249	0.91[ASN][1000 genomes]
rs2577831	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2590838	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs28661185	0.86[ASN][1000 genomes]
rs2878628	0.91[ASN][1000 genomes]
rs33964154	0.91[ASN][1000 genomes]
rs34005367	0.93[ASN][1000 genomes]
rs3796353	0.91[ASN][1000 genomes]
rs4234633	0.87[ASN][1000 genomes]
rs4282054	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4434138	0.87[ASN][1000 genomes]
rs4475032	0.93[ASN][1000 genomes]
rs4687624	0.87[ASN][1000 genomes]
rs4687625	0.93[ASN][1000 genomes]
rs4687626	0.92[ASN][1000 genomes]
rs62256903	0.92[ASN][1000 genomes]
rs6445528	0.93[ASN][1000 genomes]
rs66782572	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66824127	0.94[EUR][1000 genomes]
rs67409736	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6778735	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6778844	0.91[ASN][1000 genomes]
rs6786043	0.87[ASN][1000 genomes]
rs6786919	0.90[ASN][1000 genomes]
rs6788887	0.90[ASN][1000 genomes]
rs6788993	0.90[ASN][1000 genomes]
rs6798246	0.89[ASN][1000 genomes]
rs7614981	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636227	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7638808	0.93[ASN][1000 genomes]
rs9758945	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription 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	28 gene(s)	inside rSNPs	diseases
9	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11709284	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs11709284	NT5DC2	cis	multi-tissue	Pritchard
rs11709284	PBRM1	cis	Thyroid	GTEx
rs11709284	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs11709284	PBRM1	cis	Artery Tibial	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52533400-52559800	Weak transcription	Liver	Liver
2	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:52552000-52560800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:52552800-52560600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:52552800-52561200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:52552800-52562000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:52552800-52565400	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:52552800-52566000	Weak transcription	Stomach Mucosa	stomach
14	chr3:52552800-52566200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:52553800-52562000	Weak transcription	K562	blood
16	chr3:52554200-52566000	Weak transcription	HSMM	muscle
17	chr3:52554800-52567200	Weak transcription	Aorta	Aorta
18	chr3:52555400-52565200	Strong transcription	Fetal Intestine Small	intestine
19	chr3:52555800-52565200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:52556000-52563600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52556000-52566000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:52556200-52559800	Genic enhancers	Spleen	Spleen
23	chr3:52556200-52563800	Strong transcription	Fetal Brain Female	brain
24	chr3:52556200-52564000	Strong transcription	Brain Germinal Matrix	brain
25	chr3:52556200-52565200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:52556400-52560800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:52556400-52563600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:52556600-52564200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:52556800-52564200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:52556800-52566400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:52557000-52563800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:52557000-52565800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:52557200-52561000	Weak transcription	GM12878-XiMat	blood
34	chr3:52557200-52563400	Genic enhancers	Right Ventricle	heart
35	chr3:52557200-52563800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:52557400-52561400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:52557400-52563200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:52557400-52563400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:52557400-52563400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:52557400-52564600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr3:52557400-52564600	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr3:52557400-52565000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:52557400-52565800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:52557600-52563400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr3:52557600-52563400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:52557800-52560400	Genic enhancers	Fetal Stomach	stomach
47	chr3:52557800-52563200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:52557800-52563600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:52558000-52561600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:52558000-52563400	Strong transcription	Osteobl	bone

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