Variant report

Variant	rs35920544
Chromosome Location	chr3:52563199-52563200
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52562975-52564548	K562	blood:	n/a	n/a
2	POLR2A	chr3:52563161-52563469	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:52562836-52564910	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:52563180-52563212	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:52557221-52564466	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr3:52562638-52563327	HUVEC	blood vessel:	n/a	n/a
7	EP300	chr3:52563162-52564715	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:52557107-52565043	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:52563055-52563452	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:52562830-52564717	K562	blood:	n/a	n/a
11	POLR2A	chr3:52563148-52563354	MCF-7	breast:	n/a	n/a
12	MYC	chr3:52563176-52563285	MCF-7	breast:	n/a	n/a
13	POLR2A	chr3:52563182-52567206	K562	blood:	n/a	n/a
14	POLR2A	chr3:52560598-52572342	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:52563164-52564651	HepG2	liver:	n/a	n/a
16	MYC	chr3:52563184-52563318	MCF-7	breast:	n/a	n/a
17	POLR2A	chr3:52563026-52564606	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr3:52563160-52563257	MCF-7	breast:	n/a	n/a
19	POLR2A	chr3:52563095-52563462	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:52557044-52564804	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr3:52563102-52563392	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52541025..52543370-chr3:52561947..52564840,2	K562	blood:
2	chr3:52559482..52561203-chr3:52562436..52565441,3	MCF-7	breast:
3	chr3:52552118..52554542-chr3:52561235..52564270,3	MCF-7	breast:

No data

Variant related genes	Relation type
SMIM4	TF binding region
NT5DC2	TF binding region
ENSG00000010327	Chromatin interaction
ENSG00000168268	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510759	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1987234	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34173244	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56156188	0.83[AFR][1000 genomes]
rs56259931	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56960576	1.00[EUR][1000 genomes]
rs57008939	0.83[AFR][1000 genomes]
rs57246324	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57298447	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57319306	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57560655	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57757646	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57869735	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58100002	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58725214	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58924550	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60311166	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60415551	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60611300	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60823713	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60916588	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61538294	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes]
rs6780005	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947535	0.94[AFR][1000 genomes]
rs72947580	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950430	0.84[AFR][1000 genomes]
rs72950432	0.82[AFR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes]
rs72965177	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72965181	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73837804	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7647992	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648016	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:52552800-52565400	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:52552800-52566000	Weak transcription	Stomach Mucosa	stomach
6	chr3:52552800-52566200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:52554200-52566000	Weak transcription	HSMM	muscle
8	chr3:52554800-52567200	Weak transcription	Aorta	Aorta
9	chr3:52555400-52565200	Strong transcription	Fetal Intestine Small	intestine
10	chr3:52555800-52565200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:52556000-52563600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:52556000-52566000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:52556200-52563800	Strong transcription	Fetal Brain Female	brain
14	chr3:52556200-52564000	Strong transcription	Brain Germinal Matrix	brain
15	chr3:52556200-52565200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:52556400-52563600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:52556600-52564200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:52556800-52564200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:52556800-52566400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:52557000-52563800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:52557000-52565800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:52557200-52563400	Genic enhancers	Right Ventricle	heart
23	chr3:52557200-52563800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:52557400-52563200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:52557400-52563400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:52557400-52563400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:52557400-52564600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr3:52557400-52564600	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr3:52557400-52565000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:52557400-52565800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:52557600-52563400	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr3:52557600-52563400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:52557800-52563200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:52557800-52563600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:52558000-52563400	Strong transcription	Osteobl	bone
36	chr3:52558200-52563200	Strong transcription	NH-A	brain
37	chr3:52558200-52563600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:52558200-52566200	Genic enhancers	Fetal Lung	lung
39	chr3:52558400-52563400	Strong transcription	A549	lung
40	chr3:52558400-52566200	Weak transcription	Fetal Kidney	kidney
41	chr3:52558400-52566200	Genic enhancers	Fetal Muscle Trunk	muscle
42	chr3:52558400-52567000	Weak transcription	Small Intestine	intestine
43	chr3:52558600-52566200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:52558600-52566600	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:52558800-52566400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:52558800-52566600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr3:52559000-52566800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:52559200-52565800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:52559800-52566400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:52560000-52563400	Strong transcription	Colonic Mucosa	Colon

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