Variant report

Variant	rs2424588
Chromosome Location	chr20:23634144-23634145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23624045..23625707-chr20:23633322..23636030,2	MCF-7	breast:
2	chr20:23619975..23621824-chr20:23630879..23635181,3	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2104006	0.83[AFR][1000 genomes]
rs2145233	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2145234	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2180663	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424574	0.83[AFR][1000 genomes]
rs2424577	0.80[EUR][1000 genomes]
rs2424581	0.86[EUR][1000 genomes]
rs2983603	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2983604	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2983605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62208871	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs911122	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23622200-23636600	Weak transcription	Pancreas	Pancrea
2	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
3	chr20:23623000-23634200	Weak transcription	Right Atrium	heart
4	chr20:23623200-23636200	Weak transcription	Lung	lung
5	chr20:23628200-23638000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:23633000-23634200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr20:23633000-23635000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:23633000-23635200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr20:23633000-23636400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr20:23633000-23636600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr20:23633000-23637200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr20:23633000-23639400	Enhancers	HepG2	liver
13	chr20:23633200-23634800	Enhancers	Brain Cingulate Gyrus	brain
14	chr20:23633200-23635000	Bivalent Enhancer	Brain Hippocampus Middle	brain
15	chr20:23633200-23635000	Enhancers	HMEC	breast
16	chr20:23633200-23635400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr20:23633200-23636200	Enhancers	Brain Substantia Nigra	brain
18	chr20:23633400-23634800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr20:23633400-23635200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr20:23633400-23636000	Enhancers	Adipose Nuclei	Adipose
21	chr20:23633600-23634200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr20:23633600-23634400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr20:23633600-23634400	Enhancers	Psoas Muscle	Psoas
24	chr20:23633600-23634800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr20:23633600-23635000	Enhancers	Esophagus	oesophagus
26	chr20:23633600-23635200	Enhancers	Fetal Thymus	thymus
27	chr20:23633600-23635800	Enhancers	Colon Smooth Muscle	Colon
28	chr20:23633800-23636000	Enhancers	Brain Anterior Caudate	brain
29	chr20:23633800-23636400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr20:23634000-23634200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr20:23634000-23634800	Enhancers	Fetal Intestine Small	intestine
32	chr20:23634000-23635000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:23634000-23635000	Enhancers	Fetal Intestine Large	intestine
34	chr20:23634000-23635800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr20:23634000-23636200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr20:23634000-23636200	Enhancers	Brain Germinal Matrix	brain
37	chr20:23634000-23637400	Enhancers	Skeletal Muscle Male	skeletal muscle

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