Variant report

Variant	rs17879983
Chromosome Location	chr20:24631949-24631950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24631399..24634097-chr20:24646074..24647990,2	MCF-7	breast:
2	chr20:24625629..24628366-chr20:24631832..24633768,2	MCF-7	breast:
3	chr20:24629904..24632760-chr20:24759535..24761078,2	MCF-7	breast:
4	chr20:24629731..24632578-chr20:24657556..24659618,3	MCF-7	breast:
5	chr20:24612466..24614630-chr20:24629800..24632618,2	MCF-7	breast:
6	chr20:24631593..24633850-chr20:24634510..24636557,2	MCF-7	breast:
7	chr20:24629448..24631960-chr20:24674530..24677062,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11087473	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11696125	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4140547	0.80[EUR][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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv912824	chr20:24612808-24639916	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24615400-24633800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:24616200-24639600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr20:24620000-24641200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:24625600-24633800	Weak transcription	Spleen	Spleen
5	chr20:24628000-24633600	Enhancers	Fetal Brain Male	brain
6	chr20:24629000-24633600	Enhancers	NHLF	lung
7	chr20:24629200-24634600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:24629200-24642600	Weak transcription	Right Atrium	heart
9	chr20:24629400-24632600	Enhancers	Fetal Brain Female	brain
10	chr20:24629400-24641000	Weak transcription	Right Ventricle	heart
11	chr20:24630200-24634600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr20:24630200-24634800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:24630400-24633600	Enhancers	Placenta	Placenta
14	chr20:24630600-24632000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr20:24630600-24632200	Enhancers	HSMM	muscle
16	chr20:24630600-24632200	Enhancers	NHDF-Ad	bronchial
17	chr20:24630600-24632800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr20:24630600-24633800	Enhancers	A549	lung
19	chr20:24630600-24634400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr20:24630600-24634600	Enhancers	Muscle Satellite Cultured Cells	--
21	chr20:24630600-24634600	Enhancers	NH-A	brain
22	chr20:24630800-24632800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr20:24630800-24633000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr20:24630800-24638600	Weak transcription	Brain Substantia Nigra	brain
25	chr20:24631000-24632200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr20:24631000-24632200	Weak transcription	Brain Hippocampus Middle	brain
27	chr20:24631000-24639600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr20:24631000-24639800	Weak transcription	Brain Angular Gyrus	brain
29	chr20:24631200-24633000	Weak transcription	Fetal Muscle Leg	muscle
30	chr20:24631200-24634600	Enhancers	Gastric	stomach
31	chr20:24631200-24639600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr20:24631400-24632800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr20:24631400-24633600	Enhancers	Fetal Intestine Large	intestine
34	chr20:24631400-24635000	Enhancers	Osteobl	bone
35	chr20:24631600-24632000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr20:24631600-24632000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr20:24631600-24632000	Weak transcription	Fetal Lung	lung
38	chr20:24631600-24632000	Weak transcription	HSMMtube	muscle
39	chr20:24631600-24632400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr20:24631600-24632800	Enhancers	Stomach Mucosa	stomach
41	chr20:24631600-24637400	Weak transcription	Ovary	ovary
42	chr20:24631800-24632200	Weak transcription	Fetal Stomach	stomach
43	chr20:24631800-24632600	Enhancers	HMEC	breast

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