Variant report

Variant	rs55952796
Chromosome Location	chr3:48584737-48584738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48485511..48488053-chr3:48583832..48585803,2	K562	blood:
2	chr3:48572206..48574308-chr3:48584630..48587149,2	MCF-7	breast:
3	chr3:48504638..48507562-chr3:48580974..48584844,3	MCF-7	breast:
4	chr3:48540004..48544821-chr3:48582947..48586944,4	MCF-7	breast:
5	chr3:48546575..48548202-chr3:48583310..48585559,2	K562	blood:
6	chr3:48469345..48470998-chr3:48583885..48586226,2	K562	blood:

Variant related genes	Relation type
ENSG00000164050	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000213689	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2098101	1.00[EUR][1000 genomes]
rs28391653	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4075800	1.00[EUR][1000 genomes]
rs56073014	1.00[EUR][1000 genomes]
rs56841797	1.00[EUR][1000 genomes]
rs61368683	0.88[AFR][1000 genomes]
rs6786152	1.00[EUR][1000 genomes]
rs6787988	1.00[EUR][1000 genomes]
rs73831580	1.00[EUR][1000 genomes]
rs73831583	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839959	0.80[AFR][1000 genomes]
rs9866124	0.81[AFR][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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	esv3406976	chr3:48581748-48585946	Strong transcription Genic enhancers Weak transcription Enhancers	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48556200-48586800	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:48556400-48586400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:48559600-48586400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:48568800-48586000	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
8	chr3:48573600-48589600	Weak transcription	Fetal Lung	lung
9	chr3:48573600-48592600	Weak transcription	NHDF-Ad	bronchial
10	chr3:48573600-48593400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:48574200-48586000	Weak transcription	Primary T cells from cord blood	blood
12	chr3:48574400-48591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:48574800-48591200	Weak transcription	Dnd41	blood
14	chr3:48576000-48594000	Weak transcription	Small Intestine	intestine
15	chr3:48576400-48590200	Weak transcription	Colonic Mucosa	Colon
16	chr3:48576400-48591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:48577600-48586400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:48577600-48589600	Weak transcription	Gastric	stomach
19	chr3:48577600-48591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:48578000-48593400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:48579200-48586200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:48579800-48586000	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr3:48581000-48586000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:48581000-48591000	Weak transcription	Lung	lung
25	chr3:48581000-48593600	Weak transcription	Right Atrium	heart
26	chr3:48581200-48586000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:48581200-48586000	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:48581200-48586200	Weak transcription	Adipose Nuclei	Adipose
29	chr3:48581200-48586400	Weak transcription	Pancreas	Pancrea
30	chr3:48581200-48589400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:48581200-48593600	Weak transcription	Right Ventricle	heart
32	chr3:48581200-48593800	Weak transcription	Ovary	ovary
33	chr3:48581400-48589600	Weak transcription	HSMMtube	muscle
34	chr3:48581400-48591600	Weak transcription	Hela-S3	cervix
35	chr3:48581400-48592800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:48582600-48584800	Weak transcription	Fetal Heart	heart
37	chr3:48582600-48591800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:48582800-48585800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:48582800-48585800	Strong transcription	NHLF	lung
40	chr3:48582800-48586000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:48582800-48586600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:48583000-48586000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:48583000-48586200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:48583000-48587800	Strong transcription	Brain Germinal Matrix	brain
45	chr3:48583200-48585000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:48583200-48585000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:48583200-48585200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr3:48583200-48585600	Strong transcription	Fetal Muscle Trunk	muscle
49	chr3:48583200-48586000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:48583200-48586200	Strong transcription	Placenta	Placenta

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