Variant report

Variant	rs28478486
Chromosome Location	chr18:8074488-8074489
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12103962	0.82[AFR][1000 genomes]
rs28367342	0.82[AFR][1000 genomes]
rs28504250	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28511885	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28521877	0.82[AFR][1000 genomes]
rs28526245	0.82[AFR][1000 genomes]
rs28557220	0.88[AFR][1000 genomes]
rs28569201	0.82[AFR][1000 genomes]
rs28578123	1.00[AMR][1000 genomes]
rs28611270	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709298	0.82[AFR][1000 genomes]
rs73385648	0.82[AFR][1000 genomes]
rs73385649	0.82[AFR][1000 genomes]
rs73385658	0.82[AFR][1000 genomes]
rs73385659	0.82[AFR][1000 genomes]
rs9946952	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9948263	0.82[AFR][1000 genomes]
rs9950590	0.82[AFR][1000 genomes]
rs9952873	0.82[AFR][1000 genomes]
rs9953560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9955097	0.82[AFR][1000 genomes]
rs9957461	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9958058	0.82[AFR][1000 genomes]
rs9958245	1.00[AMR][1000 genomes]
rs9963467	0.82[AFR][1000 genomes]
rs9965217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9966934	0.82[AFR][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	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8052600-8078200	Weak transcription	Ovary	ovary
2	chr18:8052600-8105200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr18:8065600-8101600	Weak transcription	Aorta	Aorta
4	chr18:8066200-8094000	Weak transcription	Hela-S3	cervix
5	chr18:8067000-8085800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr18:8067400-8110200	Weak transcription	Right Ventricle	heart
7	chr18:8067600-8094800	Weak transcription	NHDF-Ad	bronchial
8	chr18:8067800-8081400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:8067800-8081600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr18:8068000-8078800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr18:8068000-8084000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:8068000-8085800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr18:8068000-8092400	Weak transcription	Thymus	Thymus
14	chr18:8068000-8094800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr18:8068000-8100000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr18:8068400-8078200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr18:8068400-8095200	Weak transcription	Lung	lung
18	chr18:8068400-8101600	Weak transcription	Fetal Stomach	stomach
19	chr18:8068400-8102400	Weak transcription	Fetal Thymus	thymus
20	chr18:8068600-8124800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr18:8068800-8084400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr18:8068800-8084800	Weak transcription	Fetal Heart	heart
23	chr18:8069000-8087600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr18:8069000-8102200	Weak transcription	Fetal Muscle Leg	muscle
25	chr18:8069000-8102400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr18:8069000-8102400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr18:8069400-8103400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr18:8069600-8088400	Weak transcription	HMEC	breast
29	chr18:8069600-8102400	Weak transcription	Brain Anterior Caudate	brain
30	chr18:8070000-8085800	Weak transcription	Brain Substantia Nigra	brain
31	chr18:8070000-8085800	Weak transcription	A549	lung
32	chr18:8070000-8093200	Weak transcription	Fetal Lung	lung
33	chr18:8070000-8097600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr18:8070200-8078000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr18:8070200-8085400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:8072000-8077000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr18:8072000-8079000	Weak transcription	Adipose Nuclei	Adipose
38	chr18:8073600-8074600	Enhancers	Left Ventricle	heart
39	chr18:8073800-8074800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr18:8074000-8082000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr18:8074000-8084000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr18:8074200-8102400	Weak transcription	Psoas Muscle	Psoas

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