Variant report

Variant	rs28620338
Chromosome Location	chr8:54889604-54889605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10081501	0.90[MKK][hapmap];0.95[YRI][hapmap]
rs10095679	0.81[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs10100207	0.90[MKK][hapmap];0.95[YRI][hapmap]
rs10101967	0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10112111	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10504160	0.96[LWK][hapmap];0.97[MKK][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16919753	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28374410	1.00[AMR][1000 genomes]
rs28437156	1.00[AMR][1000 genomes]
rs28452332	0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[AMR][1000 genomes]
rs28489512	1.00[AMR][1000 genomes]
rs28575670	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28698373	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28813536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs424325	1.00[CHD][hapmap]
rs56894994	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73589289	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73590828	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73590837	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73592909	0.88[AFR][1000 genomes];1.00[AMR][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	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2758160	chr8:54832990-55016965	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759617	chr8:54832990-55016965	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv427821	chr8:54832990-55016965	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54866600-54893600	Weak transcription	Fetal Kidney	kidney
2	chr8:54866800-54898000	Weak transcription	Colon Smooth Muscle	Colon
3	chr8:54866800-54898200	Weak transcription	Fetal Heart	heart
4	chr8:54868200-54895600	Weak transcription	Brain Angular Gyrus	brain
5	chr8:54871400-54891000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr8:54871400-54898000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr8:54871600-54932600	Weak transcription	Fetal Brain Male	brain
8	chr8:54872000-54892400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr8:54872800-54898200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr8:54873000-54895600	Weak transcription	Colonic Mucosa	Colon
11	chr8:54873400-54893600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr8:54873600-54894600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr8:54873600-54898000	Weak transcription	Brain Substantia Nigra	brain
14	chr8:54873800-54891000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr8:54873800-54891000	Weak transcription	NHLF	lung
16	chr8:54873800-54897400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr8:54873800-54897800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr8:54873800-54899800	Weak transcription	Right Ventricle	heart
19	chr8:54874000-54891200	Weak transcription	Esophagus	oesophagus
20	chr8:54874000-54891200	Weak transcription	Fetal Brain Female	brain
21	chr8:54874000-54896000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:54874000-54898000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:54874000-54898000	Weak transcription	Aorta	Aorta
24	chr8:54874200-54891000	Weak transcription	Brain Anterior Caudate	brain
25	chr8:54874400-54890600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr8:54874400-54890600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr8:54874400-54891000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr8:54874400-54895400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr8:54874400-54897200	Weak transcription	Brain Hippocampus Middle	brain
30	chr8:54874600-54891000	Weak transcription	Osteobl	bone
31	chr8:54875800-54898000	Weak transcription	Small Intestine	intestine
32	chr8:54876000-54890600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr8:54876000-54892000	Weak transcription	Gastric	stomach
34	chr8:54876400-54908600	Weak transcription	Psoas Muscle	Psoas
35	chr8:54876600-54890000	Weak transcription	NHDF-Ad	bronchial
36	chr8:54877000-54890200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr8:54877600-54898000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr8:54878000-54891000	Weak transcription	Left Ventricle	heart
39	chr8:54878000-54891400	Weak transcription	Pancreas	Pancrea
40	chr8:54878000-54896000	Weak transcription	Lung	lung
41	chr8:54878000-54898000	Weak transcription	Spleen	Spleen
42	chr8:54878400-54894000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr8:54879000-54890600	Weak transcription	Fetal Stomach	stomach
44	chr8:54879000-54898000	Weak transcription	HSMMtube	muscle
45	chr8:54879200-54891000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr8:54879200-54898200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr8:54880400-54906600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr8:54880400-54916000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr8:54880600-54898000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr8:54880800-54916000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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