Variant report

Variant	rs28396317
Chromosome Location	chr3:24564278-24564279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:24564266-24564280	HepG2	liver:	n/a	n/a
2	CREB1	chr3:24562627-24564285	HepG2	liver:	n/a	n/a
3	ARID3A	chr3:24563260-24565152	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:24562434-24564514	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:24529284..24531123-chr3:24562978..24564509,2	MCF-7	breast:
2	chr3:24563571..24567419-chr3:24571048..24574200,4	MCF-7	breast:
3	chr3:24534533..24538643-chr3:24561395..24564731,10	MCF-7	breast:
4	chr3:24563185..24564896-chr3:24586484..24588890,2	K562	blood:
5	chr3:24535191..24540424-chr3:24558354..24564929,10	K562	blood:
6	chr3:24563518..24566060-chr3:24581638..24584323,3	K562	blood:
7	chr3:24563518..24565481-chr3:24581638..24583515,2	K562	blood:
8	chr3:24534014..24541118-chr3:24556364..24565705,22	MCF-7	breast:
9	chr3:24513307..24515783-chr3:24564000..24565708,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4792	TF binding region
ENSG00000272554	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000151090	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13066150	1.00[EUR][1000 genomes]
rs28627946	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4330216	1.00[EUR][1000 genomes]
rs4569583	1.00[EUR][1000 genomes]
rs4858615	1.00[EUR][1000 genomes]
rs4858618	1.00[EUR][1000 genomes]
rs4858619	1.00[EUR][1000 genomes]
rs58432503	1.00[EUR][1000 genomes]
rs73150381	1.00[EUR][1000 genomes]
rs73152108	1.00[EUR][1000 genomes]
rs73152115	1.00[EUR][1000 genomes]
rs73152133	1.00[EUR][1000 genomes]
rs9819977	1.00[EUR][1000 genomes]
rs9822004	1.00[EUR][1000 genomes]
rs9882862	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 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	chr3:24562800-24568000	Enhancers	Stomach Mucosa	stomach
2	chr3:24563400-24564400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:24563800-24565800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:24564000-24564400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:24564000-24564400	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:24564000-24564400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
7	chr3:24564000-24564400	Bivalent Enhancer	A549	lung
8	chr3:24564000-24564400	Flanking Active TSS	HepG2	liver
9	chr3:24564000-24564800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:24564000-24564800	Weak transcription	Gastric	stomach
11	chr3:24564000-24565000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
12	chr3:24564000-24565000	Weak transcription	HMEC	breast
13	chr3:24564000-24565200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:24564000-24565200	Weak transcription	Hela-S3	cervix
15	chr3:24564000-24565600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:24564000-24565600	Weak transcription	HUVEC	blood vessel
17	chr3:24564000-24565600	Weak transcription	NHDF-Ad	bronchial
18	chr3:24564000-24566400	Weak transcription	Fetal Heart	heart
19	chr3:24564000-24566600	Enhancers	Liver	Liver
20	chr3:24564000-24567000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:24564000-24567000	Enhancers	Fetal Intestine Large	intestine
22	chr3:24564000-24568200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:24564000-24568400	Enhancers	Brain Germinal Matrix	brain
24	chr3:24564000-24568400	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:24564200-24564400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
26	chr3:24564200-24564400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
27	chr3:24564200-24564400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
28	chr3:24564200-24564400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:24564200-24564400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr3:24564200-24564400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:24564200-24565800	Weak transcription	K562	blood
32	chr3:24564200-24566000	Weak transcription	Psoas Muscle	Psoas
33	chr3:24564200-24567000	Enhancers	Fetal Intestine Small	intestine
34	chr3:24564200-24567600	Weak transcription	Fetal Lung	lung

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