Variant report

Variant	rs56834952
Chromosome Location	chr4:148892092-148892093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148884380..148886490-chr4:148890987..148892658,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10002792	0.81[ASN][1000 genomes]
rs10025180	0.81[ASN][1000 genomes]
rs1039660	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10519926	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11945457	0.81[ASN][1000 genomes]
rs17024212	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17024226	0.90[AFR][1000 genomes]
rs17024235	0.90[AFR][1000 genomes]
rs2306910	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2635259	0.81[ASN][1000 genomes]
rs57437177	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60635047	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7674116	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7682961	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9684012	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148859400-148898000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:148864400-148896800	Weak transcription	Osteobl	bone
3	chr4:148866400-148927400	Weak transcription	Thymus	Thymus
4	chr4:148868200-148902600	Weak transcription	NH-A	brain
5	chr4:148878400-148896400	Weak transcription	HMEC	breast
6	chr4:148878600-148896400	Weak transcription	NHEK	skin
7	chr4:148880000-148892400	Weak transcription	Psoas Muscle	Psoas
8	chr4:148880000-148892400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr4:148880200-148896600	Weak transcription	Fetal Heart	heart
10	chr4:148883400-148896400	Weak transcription	Gastric	stomach
11	chr4:148885200-148892600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr4:148885600-148905200	Weak transcription	Fetal Intestine Small	intestine
13	chr4:148885600-148905400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:148885600-148939000	Weak transcription	Pancreas	Pancrea
15	chr4:148885800-148896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:148885800-148896400	Weak transcription	Lung	lung
17	chr4:148885800-148907000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:148885800-148912800	Weak transcription	Fetal Lung	lung
19	chr4:148886000-148917600	Weak transcription	Esophagus	oesophagus
20	chr4:148886800-148901800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:148888200-148896600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr4:148888600-148896200	Weak transcription	HSMMtube	muscle
23	chr4:148888800-148896200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:148888800-148896400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:148888800-148896400	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:148889000-148896400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:148889000-148896600	Weak transcription	Aorta	Aorta
28	chr4:148889000-148905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:148889200-148899400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:148889200-148936200	Weak transcription	Fetal Intestine Large	intestine
31	chr4:148889400-148896200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:148889400-148905400	Weak transcription	NHLF	lung
33	chr4:148889600-148897000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:148889800-148896400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:148890400-148896200	Weak transcription	HSMM	muscle
36	chr4:148890400-148897800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:148890600-148892800	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr4:148890800-148892600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:148891200-148892400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:148891200-148892400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:148891200-148893000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:148891200-148896400	Weak transcription	Adipose Nuclei	Adipose
43	chr4:148891400-148892400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:148891400-148893000	Enhancers	Colon Smooth Muscle	Colon
45	chr4:148891400-148896400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:148891400-148896400	Weak transcription	Fetal Stomach	stomach
47	chr4:148891400-148896400	Weak transcription	Right Ventricle	heart
48	chr4:148891400-148905000	Weak transcription	Stomach Mucosa	stomach
49	chr4:148891400-148905400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:148891600-148892400	Weak transcription	Rectal Smooth Muscle	rectum

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