Variant report

Variant	rs28391333
Chromosome Location	chr4:56245053-56245054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr4:56245048-56245552	Hela-S3	cervix:	n/a	n/a
2	FOS	chr4:56244941-56245106	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr4:56244874-56245640	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr4:56244998-56245080	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr4:56244944-56245074	MCF10A-Er-Src	breast:	n/a	n/a
6	BRCA1	chr4:56244781-56245639	Hela-S3	cervix:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:56236823..56239564-chr4:56243563..56245351,2	MCF-7	breast:
2	chr4:56240281..56248484-chr4:56258541..56264383,10	MCF-7	breast:
3	chr4:56243121..56245532-chr4:56269359..56271036,2	MCF-7	breast:
4	chr4:56243246..56246194-chr4:56252558..56255228,2	K562	blood:
5	chr4:56232345..56235244-chr4:56243502..56246293,2	MCF-7	breast:
6	chr4:56240192..56241907-chr4:56242608..56245605,4	K562	blood:

No data

Variant related genes	Relation type
SRD5A3-AS1	TF binding region
ENSG00000273257	Chromatin interaction
ENSG00000134851	Chromatin interaction
ENSG00000249700	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10010919	0.95[AFR][1000 genomes]
rs10013154	0.85[EUR][1000 genomes]
rs10016977	0.80[AFR][1000 genomes]
rs10026202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10031345	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10155441	0.95[AFR][1000 genomes]
rs11724300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11727642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11729403	0.92[AMR][1000 genomes]
rs11732684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28369166	0.95[AFR][1000 genomes]
rs28375967	0.85[EUR][1000 genomes]
rs28418730	0.95[AFR][1000 genomes]
rs28588862	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28606621	0.80[AFR][1000 genomes]
rs28653645	0.85[EUR][1000 genomes]
rs28712413	0.80[AFR][1000 genomes]
rs28873832	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34101807	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7356345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56213800-56251400	Weak transcription	Pancreas	Pancrea
2	chr4:56214400-56247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:56228400-56245400	Weak transcription	K562	blood
4	chr4:56228400-56251000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:56230600-56245200	Weak transcription	Fetal Intestine Small	intestine
6	chr4:56232000-56247600	Weak transcription	Spleen	Spleen
7	chr4:56233200-56261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:56235800-56247600	Weak transcription	Aorta	Aorta
9	chr4:56236400-56248400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:56237000-56245400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:56237000-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:56237200-56247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:56239800-56251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:56240200-56249400	Weak transcription	Left Ventricle	heart
15	chr4:56240400-56259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:56240800-56247400	Weak transcription	Brain Angular Gyrus	brain
17	chr4:56243800-56247600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:56244000-56247800	Weak transcription	Brain Anterior Caudate	brain
19	chr4:56244200-56247400	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:56244200-56247600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:56244600-56245200	Enhancers	Brain Substantia Nigra	brain
22	chr4:56244800-56245200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:56244800-56245200	Flanking Active TSS	Hela-S3	cervix
24	chr4:56244800-56245200	Enhancers	NHEK	skin
25	chr4:56244800-56245600	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr4:56244800-56246000	Enhancers	HMEC	breast
27	chr4:56244800-56246200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:56245000-56245200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:56245000-56245200	Enhancers	Adipose Nuclei	Adipose
30	chr4:56245000-56245400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:56245000-56245400	Active TSS	Stomach Mucosa	stomach
32	chr4:56245000-56245600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr4:56245000-56245600	Enhancers	HSMMtube	muscle
34	chr4:56245000-56246000	Flanking Active TSS	A549	lung

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