Variant report

Variant	rs28434358
Chromosome Location	chr3:52417594-52417595
allele	A/G
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	chr3:52417486-52417668	MCF-7	breast:	n/a	n/a
2	E2F6	chr3:52417499-52417638	K562	blood:	n/a	n/a
3	POLR2A	chr3:52417460-52417689	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:52416968-52417672	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52406156..52409184-chr3:52415561..52421026,5	K562	blood:
2	chr3:52406883..52409184-chr3:52415694..52419355,3	K562	blood:
3	chr3:52410804..52413361-chr3:52413563..52417960,4	K562	blood:
4	chr3:52413424..52415334-chr3:52416038..52418225,2	K562	blood:

Variant related genes	Relation type
DNAH1	TF binding region
ENSG00000239557	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10212560	1.00[EUR][1000 genomes]
rs10440116	1.00[EUR][1000 genomes]
rs13318570	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28413740	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5743834	1.00[EUR][1000 genomes]
rs9813448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813489	1.00[EUR][1000 genomes]
rs9813653	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814016	1.00[EUR][1000 genomes]
rs9815559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9824342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828432	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831689	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834363	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834919	1.00[EUR][1000 genomes]
rs9836166	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842960	1.00[EUR][1000 genomes]
rs9843055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9844178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9868332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers 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	45 gene(s)	inside rSNPs	diseases
4	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
5	nsv590302	chr3:52407933-52428988	Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv3418861	chr3:52415012-52419710	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52374200-52427000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:52385400-52434600	Weak transcription	Small Intestine	intestine
3	chr3:52393200-52434800	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
5	chr3:52395400-52433200	Weak transcription	HSMMtube	muscle
6	chr3:52397800-52433000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:52398000-52425200	Weak transcription	Left Ventricle	heart
8	chr3:52403400-52433800	Weak transcription	Brain Germinal Matrix	brain
9	chr3:52405200-52425000	Weak transcription	Aorta	Aorta
10	chr3:52405400-52425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:52406400-52425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:52407200-52422200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:52407600-52420800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:52407800-52421600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:52408000-52419200	Weak transcription	Fetal Thymus	thymus
16	chr3:52408000-52421800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:52408000-52433200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:52408000-52436600	Weak transcription	Fetal Kidney	kidney
19	chr3:52408600-52421000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:52409800-52418800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:52409800-52425200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:52410000-52425200	Weak transcription	Primary B cells from cord blood	blood
23	chr3:52410000-52433200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:52410000-52434400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:52410200-52418800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:52410200-52420400	Weak transcription	Colonic Mucosa	Colon
27	chr3:52410200-52425000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:52410200-52426800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:52410400-52417800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:52410400-52418000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:52410400-52418600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:52410400-52419000	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:52410400-52419200	Weak transcription	Brain Angular Gyrus	brain
34	chr3:52410400-52419400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:52410400-52420400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr3:52410600-52419000	Weak transcription	Adipose Nuclei	Adipose
37	chr3:52410600-52419200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:52410600-52419200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:52410600-52420200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:52410600-52420200	Weak transcription	Fetal Intestine Large	intestine
41	chr3:52410600-52422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:52410600-52424800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:52410600-52425000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:52410600-52435400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:52410800-52419000	Weak transcription	Spleen	Spleen
46	chr3:52411000-52417800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:52411000-52418800	Weak transcription	Brain Anterior Caudate	brain
48	chr3:52411000-52419000	Weak transcription	Liver	Liver
49	chr3:52411000-52419400	Weak transcription	Primary T cells from cord blood	blood
50	chr3:52411000-52420200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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