Variant report

Variant	rs56954828
Chromosome Location	chr5:178373319-178373320
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10464050	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1475949	0.80[ASN][1000 genomes]
rs1475950	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17078865	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17081834	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1826862	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2132673	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56740821	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56773504	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56790802	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59485557	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59515073	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61213092	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61314110	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6867653	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6871003	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73334703	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73334721	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73334723	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73334729	0.93[ASN][1000 genomes]
rs73334737	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73336533	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73336535	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9637932	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv600489	chr5:178368096-178430375	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3322172	chr5:178370246-178374444	ZNF genes & repeats Strong transcription Weak transcription Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
3	nsv980769	chr5:178373307-178373932	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178353800-178374800	ZNF genes & repeats	Liver	Liver
2	chr5:178367000-178374600	ZNF genes & repeats	Spleen	Spleen
3	chr5:178368800-178377000	Weak transcription	Psoas Muscle	Psoas
4	chr5:178369000-178373800	Weak transcription	Brain Substantia Nigra	brain
5	chr5:178369000-178374000	Weak transcription	Osteobl	bone
6	chr5:178369000-178374400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
7	chr5:178369000-178378400	Weak transcription	NHDF-Ad	bronchial
8	chr5:178369000-178378800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:178369000-178380200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:178369000-178384800	ZNF genes & repeats	Fetal Stomach	stomach
11	chr5:178369400-178374800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:178369400-178418200	ZNF genes & repeats	Fetal Brain Female	brain
13	chr5:178369600-178373600	ZNF genes & repeats	Brain Germinal Matrix	brain
14	chr5:178369600-178374400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr5:178369600-178377400	Strong transcription	Fetal Muscle Trunk	muscle
16	chr5:178369800-178373600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:178370000-178376200	Weak transcription	Placenta	Placenta
18	chr5:178370000-178378400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:178370200-178374200	Strong transcription	Brain Anterior Caudate	brain
20	chr5:178371000-178376000	Strong transcription	Fetal Muscle Leg	muscle
21	chr5:178371000-178376000	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr5:178371200-178373600	ZNF genes & repeats	Brain Hippocampus Middle	brain
23	chr5:178371200-178374200	Strong transcription	Brain Angular Gyrus	brain
24	chr5:178371200-178374800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr5:178371200-178375800	ZNF genes & repeats	Aorta	Aorta
26	chr5:178371200-178379200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr5:178371400-178375800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:178371600-178375600	ZNF genes & repeats	Esophagus	oesophagus
29	chr5:178371800-178373400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
30	chr5:178371800-178373400	ZNF genes & repeats	Fetal Intestine Large	intestine
31	chr5:178371800-178378000	ZNF genes & repeats	Fetal Intestine Small	intestine
32	chr5:178372200-178374600	ZNF genes & repeats	Lung	lung
33	chr5:178372200-178375600	Strong transcription	Right Ventricle	heart
34	chr5:178372400-178374600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:178372400-178374800	ZNF genes & repeats	Gastric	stomach
36	chr5:178372400-178375800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr5:178372400-178375800	ZNF genes & repeats	Adipose Nuclei	Adipose
38	chr5:178372400-178376400	ZNF genes & repeats	Pancreas	Pancrea
39	chr5:178372600-178374200	Strong transcription	Left Ventricle	heart
40	chr5:178372600-178374600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:178372600-178375600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:178372600-178377400	Weak transcription	Fetal Heart	heart
43	chr5:178372800-178374000	Weak transcription	Fetal Kidney	kidney
44	chr5:178372800-178374200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr5:178372800-178374400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:178372800-178375600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:178372800-178375600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:178373000-178373800	Weak transcription	Fetal Brain Male	brain
49	chr5:178373000-178374200	Strong transcription	Pancreatic Islets	Pancreatic Islet
50	chr5:178373000-178374600	Strong transcription	Colon Smooth Muscle	Colon

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