Variant report

Variant	rs55871529
Chromosome Location	chr3:119896959-119896960
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119896267..119897823-chr3:119902121..119903746,2	MCF-7	breast:
2	chr3:119810057..119817149-chr3:119894256..119903865,22	MCF-7	breast:
3	chr3:119809943..119817218-chr3:119893934..119905581,30	MCF-7	breast:
4	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:
5	chr3:119877444..119878944-chr3:119896183..119899107,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1079784	0.87[AMR][1000 genomes]
rs10934520	0.85[AMR][1000 genomes]
rs13064815	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079094	0.83[AMR][1000 genomes]
rs2029607	0.85[AMR][1000 genomes]
rs34032950	0.87[AMR][1000 genomes]
rs34537735	0.83[AMR][1000 genomes]
rs34720062	0.87[AMR][1000 genomes]
rs35193138	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35280462	0.87[AMR][1000 genomes]
rs35791817	0.85[AMR][1000 genomes]
rs35902169	0.85[AMR][1000 genomes]
rs35977875	0.87[AMR][1000 genomes]
rs7630226	0.85[AMR][1000 genomes]
rs7633395	0.83[AMR][1000 genomes]
rs7634938	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119892400-119914200	Weak transcription	Fetal Brain Female	brain
2	chr3:119893600-119897400	Enhancers	Placenta	Placenta
3	chr3:119895200-119897200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:119895400-119897000	Enhancers	Psoas Muscle	Psoas
5	chr3:119895400-119897200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:119895600-119897000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:119895600-119897000	Enhancers	Fetal Muscle Leg	muscle
8	chr3:119895600-119897000	Enhancers	Right Ventricle	heart
9	chr3:119895600-119897000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:119895600-119897000	Flanking Active TSS	A549	lung
11	chr3:119895600-119897000	Flanking Active TSS	Hela-S3	cervix
12	chr3:119895600-119897200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:119895800-119897000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:119895800-119897000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:119895800-119897000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:119895800-119897000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:119895800-119897000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:119895800-119897000	Enhancers	Colon Smooth Muscle	Colon
19	chr3:119895800-119897000	Enhancers	Fetal Lung	lung
20	chr3:119895800-119897000	Enhancers	Rectal Smooth Muscle	rectum
21	chr3:119895800-119897000	Enhancers	HSMM	muscle
22	chr3:119896000-119897000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:119896000-119897000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:119896000-119897000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr3:119896000-119897000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:119896000-119897000	Enhancers	Fetal Stomach	stomach
27	chr3:119896000-119897000	Enhancers	Right Atrium	heart
28	chr3:119896000-119897000	Flanking Active TSS	Osteobl	bone
29	chr3:119896200-119897000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:119896200-119897000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:119896200-119897000	Enhancers	Aorta	Aorta
32	chr3:119896200-119897000	Flanking Active TSS	NHDF-Ad	bronchial
33	chr3:119896200-119897000	Flanking Active TSS	NHLF	lung
34	chr3:119896200-119897200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr3:119896200-119900000	Weak transcription	Fetal Intestine Small	intestine
36	chr3:119896400-119897000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr3:119896400-119897000	Enhancers	Adipose Nuclei	Adipose
38	chr3:119896400-119897000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:119896400-119897000	Enhancers	HepG2	liver
40	chr3:119896400-119897200	Enhancers	NHEK	skin
41	chr3:119896400-119899600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:119896400-119900000	Weak transcription	Esophagus	oesophagus
43	chr3:119896400-119921400	Weak transcription	Ovary	ovary
44	chr3:119896600-119897000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:119896600-119897000	Enhancers	HSMMtube	muscle
46	chr3:119896600-119897200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:119896600-119897200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:119896600-119897200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:119896600-119897200	Enhancers	HUVEC	blood vessel
50	chr3:119896800-119897000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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