Variant report

Variant	rs72947531
Chromosome Location	chr3:52554208-52554209
allele	C/T
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	chr3:52554098-52554284	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:52554045-52554255	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52551111..52554473-chr3:52556873..52560591,3	MCF-7	breast:
2	chr3:52553170..52556656-chr3:52557821..52561228,3	MCF-7	breast:
3	chr3:52552118..52554542-chr3:52561235..52564270,3	MCF-7	breast:

Variant related genes	Relation type
STAB1	TF binding region
ENSG00000168268	Chromatin interaction
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13066389	0.80[AFR][1000 genomes]
rs17052326	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052421	1.00[EUR][1000 genomes]
rs2577828	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2577829	1.00[EUR][1000 genomes]
rs2577830	1.00[EUR][1000 genomes]
rs2577838	0.83[AFR][1000 genomes]
rs2590840	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2590841	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs36010847	1.00[AMR][1000 genomes]
rs4234635	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4234636	1.00[EUR][1000 genomes]
rs56866386	1.00[EUR][1000 genomes]
rs61734654	1.00[AMR][1000 genomes]
rs6766038	1.00[EUR][1000 genomes]
rs6771643	1.00[AMR][1000 genomes]
rs6786835	1.00[AMR][1000 genomes]
rs6787806	1.00[AMR][1000 genomes]
rs6788355	1.00[AMR][1000 genomes]
rs6794706	1.00[EUR][1000 genomes]
rs72947525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72947530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72947532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72947537	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72947557	1.00[EUR][1000 genomes]
rs72959348	1.00[EUR][1000 genomes]
rs72965274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7614424	0.80[AFR][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	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	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:52533400-52559800	Weak transcription	Liver	Liver
4	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:52542000-52557400	Weak transcription	Thymus	Thymus
10	chr3:52544000-52557400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:52550800-52558400	Strong transcription	HUVEC	blood vessel
13	chr3:52551000-52554600	Genic enhancers	Spleen	Spleen
14	chr3:52552000-52560800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:52552400-52559200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:52552600-52558200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:52552800-52556600	Weak transcription	Left Ventricle	heart
18	chr3:52552800-52557600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:52552800-52557600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:52552800-52557800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:52552800-52557800	Weak transcription	NHEK	skin
22	chr3:52552800-52558200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:52552800-52560600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:52552800-52561200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:52552800-52562000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:52552800-52565400	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:52552800-52566000	Weak transcription	Stomach Mucosa	stomach
28	chr3:52552800-52566200	Weak transcription	Brain Angular Gyrus	brain
29	chr3:52553000-52558400	Weak transcription	Brain Substantia Nigra	brain
30	chr3:52553000-52558400	Strong transcription	Lung	lung
31	chr3:52553200-52555400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:52553200-52555800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:52553200-52556000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:52553200-52556200	Weak transcription	Brain Germinal Matrix	brain
35	chr3:52553200-52556400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:52553200-52556800	Weak transcription	Fetal Intestine Large	intestine
37	chr3:52553200-52557400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:52553200-52557400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:52553200-52557800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:52553200-52557800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:52553200-52557800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr3:52553200-52558000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:52553200-52558000	Weak transcription	Osteobl	bone
44	chr3:52553200-52558400	Weak transcription	A549	lung
45	chr3:52553200-52559400	Weak transcription	Brain Anterior Caudate	brain
46	chr3:52553400-52554400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:52553400-52555400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:52553400-52555400	Weak transcription	Fetal Intestine Small	intestine
49	chr3:52553400-52556200	Weak transcription	Fetal Brain Female	brain
50	chr3:52553400-52556600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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