Variant report

Variant	rs58877857
Chromosome Location	chr4:90687134-90687135
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10516846	0.99[AFR][1000 genomes]
rs10516847	0.96[AFR][1000 genomes]
rs17016083	0.88[AFR][1000 genomes]
rs17016107	0.83[AMR][1000 genomes]
rs17016124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17016126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17016196	0.93[AFR][1000 genomes]
rs34094566	0.82[AFR][1000 genomes]
rs34351491	0.88[AFR][1000 genomes]
rs34356244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34747217	0.82[AFR][1000 genomes]
rs35540244	0.92[AFR][1000 genomes]
rs35683448	0.88[AFR][1000 genomes]
rs35771728	0.82[AFR][1000 genomes]
rs35921673	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs3729594	0.96[AFR][1000 genomes]
rs3775435	0.96[AFR][1000 genomes]
rs3775437	0.96[AFR][1000 genomes]
rs3775438	0.89[AFR][1000 genomes]
rs3775442	0.96[AFR][1000 genomes]
rs3775444	0.93[AFR][1000 genomes]
rs3775450	0.94[AFR][1000 genomes]
rs3796662	0.92[AFR][1000 genomes]
rs3822088	0.96[AFR][1000 genomes]
rs3822091	0.96[AFR][1000 genomes]
rs3857054	0.82[AFR][1000 genomes]
rs3857056	0.82[AFR][1000 genomes]
rs3857060	0.83[AFR][1000 genomes]
rs3898322	0.96[AFR][1000 genomes]
rs4635786	0.82[AFR][1000 genomes]
rs57267227	0.82[AFR][1000 genomes]
rs57928386	0.82[AFR][1000 genomes]
rs61378184	0.82[AFR][1000 genomes]
rs6825073	0.99[AFR][1000 genomes]
rs72657741	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7699596	0.99[AFR][1000 genomes]
rs961386	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr4:90649400-90696400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:90663400-90691400	Weak transcription	Dnd41	blood
3	chr4:90675400-90696200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:90676200-90709200	Weak transcription	HUVEC	blood vessel
5	chr4:90683600-90687200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:90683600-90689200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:90684600-90687200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:90685200-90696400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:90686000-90687800	Enhancers	Brain Hippocampus Middle	brain
10	chr4:90686200-90687600	Enhancers	Brain Anterior Caudate	brain
11	chr4:90686200-90687600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr4:90686200-90688200	Enhancers	Brain Substantia Nigra	brain
13	chr4:90686400-90687400	Enhancers	Left Ventricle	heart
14	chr4:90686400-90687400	Enhancers	Rectal Smooth Muscle	rectum
15	chr4:90686400-90687600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:90686400-90687600	Enhancers	NHEK	skin
17	chr4:90686800-90687200	Enhancers	Brain Angular Gyrus	brain
18	chr4:90686800-90687200	Enhancers	HSMM	muscle
19	chr4:90686800-90687200	Enhancers	HSMMtube	muscle
20	chr4:90686800-90687400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr4:90686800-90687400	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:90686800-90687400	Enhancers	HMEC	breast
23	chr4:90686800-90687400	Enhancers	NH-A	brain
24	chr4:90686800-90687600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:90686800-90687600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:90686800-90687600	Enhancers	Fetal Stomach	stomach
27	chr4:90686800-90687800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:90686800-90687800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:90686800-90687800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:90686800-90687800	Enhancers	Fetal Heart	heart
31	chr4:90686800-90688000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr4:90687000-90687200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:90687000-90687200	Active TSS	Fetal Brain Male	brain
34	chr4:90687000-90687400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:90687000-90687400	Enhancers	Brain Germinal Matrix	brain
36	chr4:90687000-90687400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr4:90687000-90687400	Enhancers	Fetal Brain Female	brain
38	chr4:90687000-90687400	Enhancers	Fetal Kidney	kidney
39	chr4:90687000-90687400	Flanking Active TSS	Fetal Lung	lung
40	chr4:90687000-90687400	Enhancers	Hela-S3	cervix
41	chr4:90687000-90687600	Enhancers	Adipose Nuclei	Adipose
42	chr4:90687000-90688000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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